Package evaluation of SpineBasedRecordLinkage on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T08:19:35.487


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# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 5.26s


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# Installation
#

Installing SpineBasedRecordLinkage...
   Resolving package versions...
    Updating `~/.julia/environments/v1.10/Project.toml`
  [c1ccfb80] + SpineBasedRecordLinkage v0.4.2
    Updating `~/.julia/environments/v1.10/Manifest.toml`
⌅ [336ed68f] + CSV v0.9.11
  [324d7699] + CategoricalArrays v0.10.8
  [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 v0.18.20
  [e2d170a0] + DataValueInterfaces v1.0.0
  [b4f34e82] + Distances v0.10.12
  [48062228] + FilePathsBase v0.9.23
  [842dd82b] + InlineStrings v1.4.3
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.0
  [69de0a69] + Parsers v2.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.0
  [b4d66a32] + Schemata v3.0.2
  [91c51154] + SentinelArrays v1.4.8
  [a2af1166] + SortingAlgorithms v1.2.1
  [c1ccfb80] + SpineBasedRecordLinkage v0.4.2
  [82ae8749] + StatsAPI v1.7.0
  [88034a9c] + StringDistances v0.11.3
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [ea10d353] + WeakRefStrings v1.4.2
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [de0858da] + Printf
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+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 5.25s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 33.73s


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# Testing
#

     Testing SpineBasedRecordLinkage
      Status `/tmp/jl_LGLfk2/Project.toml`
⌅ [336ed68f] CSV v0.9.11
  [a93c6f00] DataFrames v1.7.0
  [b4d66a32] Schemata v3.0.2
  [c1ccfb80] SpineBasedRecordLinkage v0.4.2
  [8dfed614] Test
      Status `/tmp/jl_LGLfk2/Manifest.toml`
⌅ [336ed68f] CSV v0.9.11
  [324d7699] CategoricalArrays v0.10.8
  [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 v0.18.20
  [e2d170a0] DataValueInterfaces v1.0.0
  [b4f34e82] Distances v0.10.12
  [48062228] FilePathsBase v0.9.23
  [842dd82b] InlineStrings v1.4.3
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [b964fa9f] LaTeXStrings v1.4.0
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.0
  [69de0a69] Parsers v2.8.1
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [b4d66a32] Schemata v3.0.2
  [91c51154] SentinelArrays v1.4.8
  [a2af1166] SortingAlgorithms v1.2.1
  [c1ccfb80] SpineBasedRecordLinkage v0.4.2
  [82ae8749] StatsAPI v1.7.0
  [88034a9c] StringDistances v0.11.3
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [ea10d353] WeakRefStrings v1.4.2
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [de0858da] Printf
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] OpenBLAS_jll v0.3.23+4
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...

TEST SET 1
Write LinkageConfig
Construct spine from influenza cases
[ Info: 2025-02-25T08:20:57.809 Configuring linkage
[ Info: 2025-02-25T08:20:59.503 Initialising output directory: output/linkage-influenza-cases-spine-2025.02.25T08.21.00
[ Info: 2025-02-25T08:21:01.547 Initialising spine
[ Info: 2025-02-25T08:21:01.905 Starting linkage for table influenza_cases
[ Info: 2025-02-25T08:21:36.930 Exported 8 rows of influenza_cases
[ Info: 2025-02-25T08:21:37.188 Exported 8 links between influenza_cases and the spine
[ Info: 2025-02-25T08:21:37.188 Writing spine to the output directory (4 rows)
[ Info: 2025-02-25T08:21:37.419 Finished linkage
Link influenza cases to events
[ Info: 2025-02-25T08:21:42.117 Configuring linkage
[ Info: 2025-02-25T08:21:42.175 Initialising output directory: output/linkage-influenza-cases-link-2025.02.25T08.21.42
[ Info: 2025-02-25T08:21:42.177 Importing spine
[ Info: 2025-02-25T08:21:42.926 Starting linkage for table emergency_presentations
[ Info: 2025-02-25T08:21:44.656 Exported 5 rows of emergency_presentations
[ Info: 2025-02-25T08:21:44.656 Exported 3 links between emergency_presentations and the spine
[ Info: 2025-02-25T08:21:44.656 Starting linkage for table hospital_admissions
[ Info: 2025-02-25T08:21:45.055 Exported 5 rows of hospital_admissions
[ Info: 2025-02-25T08:21:45.055 Exported 3 links between hospital_admissions and the spine
[ Info: 2025-02-25T08:21:45.055 Starting linkage for table influenza_cases
[ Info: 2025-02-25T08:21:46.357 Exported 8 rows of influenza_cases
[ Info: 2025-02-25T08:21:46.357 Exported 8 links between influenza_cases and the spine
[ Info: 2025-02-25T08:21:46.357 Writing spine to the output directory (4 rows)
[ Info: 2025-02-25T08:21:46.524 Finished linkage
Reporting
[ Info: 2025-02-25T08:21:53.045 Starting summary of linkage run.
[ Info: 2025-02-25T08:21:54.605 Reporting results for table emergency_presentations
[ Info: 2025-02-25T08:21:54.827 Reporting results for table hospital_admissions
[ Info: 2025-02-25T08:21:54.882 Reporting results for table influenza_cases
[ Info: 2025-02-25T08:21:54.987 Reporting results for table spine
[ Info: 2025-02-25T08:21:56.814 Finished summary of linkage run.

TEST SET 2
Link all health service events
[ Info: 2025-02-25T08:21:58.531 Configuring linkage
[ Info: 2025-02-25T08:21:58.534 Initialising output directory: output/linkage-health-service-usage-2025.02.25T08.21.59
[ Info: 2025-02-25T08:21:58.535 Initialising spine
[ Info: 2025-02-25T08:21:58.571 Starting linkage for table hospital_admissions
[ Info: 2025-02-25T08:21:58.686 Exported 5 rows of hospital_admissions
[ Info: 2025-02-25T08:21:58.686 Exported 5 links between hospital_admissions and the spine
[ Info: 2025-02-25T08:21:58.686 Starting linkage for table emergency_presentations
[ Info: 2025-02-25T08:21:59.271 Exported 5 rows of emergency_presentations
[ Info: 2025-02-25T08:21:59.272 Exported 5 links between emergency_presentations and the spine
[ Info: 2025-02-25T08:21:59.272 Starting linkage for table influenza_cases
[ Info: 2025-02-25T08:21:59.316 Exported 8 rows of influenza_cases
[ Info: 2025-02-25T08:21:59.317 Exported 8 links between influenza_cases and the spine
[ Info: 2025-02-25T08:21:59.317 Writing spine to the output directory (6 rows)
[ Info: 2025-02-25T08:21:59.569 Finished linkage
Reporting
[ Info: 2025-02-25T08:21:59.570 Starting summary of linkage run.
[ Info: 2025-02-25T08:21:59.571 Reporting results for table emergency_presentations
[ Info: 2025-02-25T08:21:59.575 Reporting results for table hospital_admissions
[ Info: 2025-02-25T08:21:59.580 Reporting results for table influenza_cases
[ Info: 2025-02-25T08:21:59.584 Reporting results for table spine
[ Info: 2025-02-25T08:21:59.587 Finished summary of linkage run.

TEST SET 3
[ Info: 2025-02-25T08:21:59.669 Starting comparison of linkage runs.
[ Info: 2025-02-25T08:22:00.202 Reporting results for table emergency_presentations
[ Info: 2025-02-25T08:22:00.267 Reporting results for table hospital_admissions
[ Info: 2025-02-25T08:22:00.276 Reporting results for table influenza_cases
[ Info: 2025-02-25T08:22:00.285 Reporting results for table spine
[ Info: 2025-02-25T08:22:00.289 Finished comparison of linkage runs.
     Testing SpineBasedRecordLinkage tests passed 

Testing completed after 99.44s

PkgEval succeeded after 147.82s