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1.5.2-pre-be8475f41a.log
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Julia Version 1.5.2-pre.25
Commit be8475f41a (2020-09-09 06:41 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake-avx512)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed OMOPCommonDataModel ─ v0.1.4
Installed DocStringExtensions ─ v0.8.3
Updating `~/.julia/environments/v1.5/Project.toml`
[ba65db9e] + OMOPCommonDataModel v0.1.4
Updating `~/.julia/environments/v1.5/Manifest.toml`
[ffbed154] + DocStringExtensions v0.8.3
[ba65db9e] + OMOPCommonDataModel v0.1.4
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[56ddb016] + Logging
[d6f4376e] + Markdown
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Testing OMOPCommonDataModel
Status `/tmp/jl_uBy1Gu/Project.toml`
[a93c6f00] DataFrames v0.21.7
[ffbed154] DocStringExtensions v0.8.3
[e30172f5] Documenter v0.25.2
[ba65db9e] OMOPCommonDataModel v0.1.4
[8162dcfd] PrettyPrint v0.2.0
[09ab397b] StructArrays v0.4.4
[bd369af6] Tables v1.0.5
[ade2ca70] Dates
[44cfe95a] Pkg
[8dfed614] Test
Status `/tmp/jl_uBy1Gu/Manifest.toml`
[79e6a3ab] Adapt v2.0.2
[324d7699] CategoricalArrays v0.8.2
[34da2185] Compat v3.15.0
[9a962f9c] DataAPI v1.3.0
[a93c6f00] DataFrames v0.21.7
[864edb3b] DataStructures v0.18.4
[e2d170a0] DataValueInterfaces v1.0.0
[ffbed154] DocStringExtensions v0.8.3
[e30172f5] Documenter v0.25.2
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.1
[e1d29d7a] Missings v0.4.4
[ba65db9e] OMOPCommonDataModel v0.1.4
[bac558e1] OrderedCollections v1.3.0
[69de0a69] Parsers v1.0.10
[2dfb63ee] PooledArrays v0.5.3
[8162dcfd] PrettyPrint v0.2.0
[189a3867] Reexport v0.2.0
[a2af1166] SortingAlgorithms v0.3.1
[09ab397b] StructArrays v0.4.4
[856f2bd8] StructTypes v1.1.0
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v1.0.5
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
WARNING: Method definition (::Type{Base.OrderStyle})(Type{Union{}}) in module Base at traits.jl:12 overwritten in module CategoricalArrays at /home/pkgeval/.julia/packages/CategoricalArrays/hxUIH/src/CategoricalArrays.jl:19.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition (::Type{Base.OrderStyle})(Type{Union{}}) in module Base at traits.jl:12 overwritten in module CategoricalArrays at /home/pkgeval/.julia/packages/CategoricalArrays/hxUIH/src/CategoricalArrays.jl:19.
** incremental compilation may be fatally broken for this module **
[ Info: Reading from input file "/home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/assets/OMOP-CDM-sql-server-ddl.txt"
[ Info: Generated 39 types
[ Info: Wrote to output file "/tmp/jl_i3NRn9/autogenerated.jl"
[ Info: Reading from input file "/home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/assets/OMOP-CDM-sql-server-ddl.txt"
[ Info: Generated 39 types
[ Info: Wrote to output file "/tmp/jl_i3NRn9/autogenerated.jl"
[ Info: Reading from input file "/home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/assets/OMOP-CDM-sql-server-ddl.txt"
[ Info: Generated 39 types
[ Info: Wrote to output file "/tmp/jl_i3NRn9/autogenerated.jl"
[ Info: Reading from input file "/home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/assets/OMOP-CDM-sql-server-ddl.txt"
[ Info: Generated 39 types
[ Info: Wrote to output file "/tmp/jl_i3NRn9/autogenerated.jl"
[ Info: Reading from input file "/home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/assets/OMOP-CDM-sql-server-ddl.txt"
[ Info: Generated 39 types
[ Info: Wrote to output file "/tmp/jl_i3NRn9/autogenerated.jl"
[ Info: Reading from input file "/home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/assets/OMOP-CDM-sql-server-ddl.txt"
[ Info: Generated 39 types
[ Info: Wrote to output file "/tmp/jl_i3NRn9/autogenerated.jl"
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
┌ Error: doctest failure in ~/.julia/packages/OMOPCommonDataModel/PUS0q/docs/src/examples.md:7-76
│
│ ```jldoctest
│ julia> using OMOPCommonDataModel
│
│ julia> using DataFrames, PrettyPrint, StructArrays, Tables
│
│ julia> jack = Person(person_id = 1, gender_concept_id = 12, year_of_birth = 1900, race_concept_id = 21, ethnicity_concept_id = 31, gender_source_concept_id = 42, race_source_concept_id = 51, ethnicity_source_concept_id = 61)
│ Person(1, 12, 1900, missing, missing, missing, 21, 31, missing, missing, missing, missing, missing, 42, missing, 51, missing, 61)
│
│ julia> jill = Person(person_id = 2, gender_concept_id = 11, year_of_birth = 1900, month_of_birth = 1, day_of_birth = 1, race_concept_id = 22, ethnicity_concept_id = 32, gender_source_concept_id = 41, race_source_concept_id = 52, ethnicity_source_concept_id = 62)
│ Person(2, 11, 1900, 1, 1, missing, 22, 32, missing, missing, missing, missing, missing, 41, missing, 52, missing, 62)
│
│ julia> pprint(jack)
│ Person(
│ person_id=1,
│ gender_concept_id=12,
│ year_of_birth=1900,
│ month_of_birth=Missing(),
│ day_of_birth=Missing(),
│ birth_datetime=Missing(),
│ race_concept_id=21,
│ ethnicity_concept_id=31,
│ location_id=Missing(),
│ provider_id=Missing(),
│ care_site_id=Missing(),
│ person_source_value=Missing(),
│ gender_source_value=Missing(),
│ gender_source_concept_id=42,
│ race_source_value=Missing(),
│ race_source_concept_id=51,
│ ethnicity_source_value=Missing(),
│ ethnicity_source_concept_id=61,
│ )
│
│ julia> pprint(jill)
│ Person(
│ person_id=2,
│ gender_concept_id=11,
│ year_of_birth=1900,
│ month_of_birth=1,
│ day_of_birth=1,
│ birth_datetime=Missing(),
│ race_concept_id=22,
│ ethnicity_concept_id=32,
│ location_id=Missing(),
│ provider_id=Missing(),
│ care_site_id=Missing(),
│ person_source_value=Missing(),
│ gender_source_value=Missing(),
│ gender_source_concept_id=41,
│ race_source_value=Missing(),
│ race_source_concept_id=52,
│ ethnicity_source_value=Missing(),
│ ethnicity_source_concept_id=62,
│ )
│
│ julia> person_table = StructArray(Person[jack, jill])
│ 2-element StructArray(::Vector{Int64}, ::Vector{Int64}, ::Vector{Int64}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Dates.DateTime}}, ::Vector{Int64}, ::Vector{Int64}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}) with eltype Person:
│ Person(1, 12, 1900, missing, missing, missing, 21, 31, missing, missing, missing, missing, missing, 42, missing, 51, missing, 61)
│ Person(2, 11, 1900, 1, 1, missing, 22, 32, missing, missing, missing, missing, missing, 41, missing, 52, missing, 62)
│
│ julia> person_table_df = DataFrame(person_table);
│
│ julia> @show(person_table_df);
│ person_table_df = 2×18 DataFrame
│ │ Row │ person_id │ gender_concept_id │ year_of_birth │ month_of_birth │ day_of_birth │ birth_datetime │ race_concept_id │ ethnicity_concept_id │ location_id │ provider_id │ care_site_id │ person_source_value │ gender_source_value │ gender_source_concept_id │ race_source_value │ race_source_concept_id │ ethnicity_source_value │ ethnicity_source_concept_id │
│ │ │ Int64 │ Int64 │ Int64 │ Int64? │ Int64? │ DateTime…? │ Int64 │ Int64 │ Int64? │ Int64? │ Int64? │ String? │ String? │ Union{Missing, Int64} │ String? │ Union{Missing, Int64} │ Union{Missing, String} │ Union{Missing, Int64} │
│ ├─────┼───────────┼───────────────────┼───────────────┼────────────────┼──────────────┼────────────────┼─────────────────┼──────────────────────┼─────────────┼─────────────┼──────────────┼─────────────────────┼─────────────────────┼──────────────────────────┼───────────────────┼────────────────────────┼────────────────────────┼─────────────────────────────┤
│ │ 1 │ 1 │ 12 │ 1900 │ missing │ missing │ missing │ 21 │ 31 │ missing │ missing │ missing │ missing │ missing │ 42 │ missing │ 51 │ missing │ 61 │
│ │ 2 │ 2 │ 11 │ 1900 │ 1 │ 1 │ missing │ 22 │ 32 │ missing │ missing │ missing │ missing │ missing │ 41 │ missing │ 52 │ missing │ 62 │
│ ```
│
│ Subexpression:
│
│ person_table = StructArray(Person[jack, jill])
│
│ Evaluated output:
│
│ 2-element StructArray(::Array{Int64,1}, ::Array{Int64,1}, ::Array{Int64,1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Dates.DateTime},1}, ::Array{Int64,1}, ::Array{Int64,1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, Int64},1}) with eltype Person:
│ Person(1, 12, 1900, missing, missing, missing, 21, 31, missing, missing, missing, missing, missing, 42, missing, 51, missing, 61)
│ Person(2, 11, 1900, 1, 1, missing, 22, 32, missing, missing, missing, missing, missing, 41, missing, 52, missing, 62)
│
│ Expected output:
│
│ 2-element StructArray(::Vector{Int64}, ::Vector{Int64}, ::Vector{Int64}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Dates.DateTime}}, ::Vector{Int64}, ::Vector{Int64}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}) with eltype Person:
│ Person(1, 12, 1900, missing, missing, missing, 21, 31, missing, missing, missing, missing, missing, 42, missing, 51, missing, 61)
│ Person(2, 11, 1900, 1, 1, missing, 22, 32, missing, missing, missing, missing, missing, 41, missing, 52, missing, 62)
│
│ diff =
│ Warning: Diff output requires color.
│ 2-element StructArray(::Vector{Int64}, ::Vector{Int64}, ::Vector{Int64}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Dates.DateTime}}, ::Vector{Int64}, ::Vector{Int64}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}, ::Vector{Union{Missing, String}}, ::Vector{Union{Missing, Int64}}) StructArray(::Array{Int64,1}, ::Array{Int64,1}, ::Array{Int64,1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Dates.DateTime},1}, ::Array{Int64,1}, ::Array{Int64,1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, Int64},1}, ::Array{Union{Missing, String},1}, ::Array{Union{Missing, Int64},1}) with eltype Person:
│ Person(1, 12, 1900, missing, missing, missing, 21, 31, missing, missing, missing, missing, missing, 42, missing, 51, missing, 61)
│ Person(2, 11, 1900, 1, 1, missing, 22, 32, missing, missing, missing, missing, missing, 41, missing, 52, missing, 62)
└ @ Documenter.DocTests ~/.julia/packages/Documenter/pjwqp/src/DocTests.jl:369
┌ Error: Doctesting failed
│ exception =
│ `makedocs` encountered a doctest error. Terminating build
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] runner(::Type{Documenter.Builder.Doctest}, ::Documenter.Documents.Document) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Builder.jl:217
│ [3] dispatch(::Type{Documenter.Builder.DocumentPipeline}, ::Documenter.Documents.Document) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Utilities/Selectors.jl:167
│ [4] #2 at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:241 [inlined]
│ [5] cd(::Documenter.var"#2#3"{Documenter.Documents.Document}, ::String) at ./file.jl:104
│ [6] makedocs(; debug::Bool, format::Documenter.Writers.HTMLWriter.HTML, kwargs::Base.Iterators.Pairs{Symbol,Any,NTuple{5,Symbol},NamedTuple{(:root, :source, :sitename, :doctest, :modules),Tuple{String,String,String,Symbol,Array{Module,1}}}}) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:240
│ [7] (::Documenter.var"#all_doctests#31"{Bool,Array{Module,1}})() at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:802
│ [8] macro expansion at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:818 [inlined]
│ [9] macro expansion at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1115 [inlined]
│ [10] doctest(::String, ::Array{Module,1}; fix::Bool, testset::String) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:818
│ [11] doctest(::Module; manual::Bool, testset::Nothing, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:761
│ [12] doctest(::Module) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:748
│ [13] top-level scope at /home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/test/runtests.jl:113
│ [14] top-level scope at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1115
│ [15] top-level scope at /home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/test/runtests.jl:113
│ [16] top-level scope at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1115
│ [17] top-level scope at /home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/test/runtests.jl:11
│ [18] include(::String) at ./client.jl:457
│ [19] top-level scope at none:6
│ [20] eval(::Module, ::Any) at ./boot.jl:331
│ [21] exec_options(::Base.JLOptions) at ./client.jl:272
│ [22] _start() at ./client.jl:506
└ @ Documenter ~/.julia/packages/Documenter/pjwqp/src/Documenter.jl:811
Doctests: OMOPCommonDataModel: Test Failed at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:818
Expression: all_doctests()
Stacktrace:
[1] macro expansion at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:818 [inlined]
[2] macro expansion at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1115 [inlined]
[3] doctest(::String, ::Array{Module,1}; fix::Bool, testset::String) at /home/pkgeval/.julia/packages/Documenter/pjwqp/src/Documenter.jl:818
Test Summary: | Pass Fail Total
OMOPCommonDataModel.jl | 89 1 90
Unit tests | 89 89
Doctests | 1 1
Doctests: OMOPCommonDataModel | 1 1
ERROR: LoadError: Some tests did not pass: 89 passed, 1 failed, 0 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/OMOPCommonDataModel/PUS0q/test/runtests.jl:10
ERROR: Package OMOPCommonDataModel errored during testing
Stacktrace:
[1] pkgerror(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:52
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1578
[3] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:328
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:315
[5] #test#61 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:67 [inlined]
[6] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:67 [inlined]
[7] #test#60 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:66 [inlined]
[8] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:66 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:65
[10] test(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:65
[11] top-level scope at none:19