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1.5.0-DEV-ed177d17d6.log
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Julia Version 1.5.0-DEV.158
Commit ed177d17d6 (2020-01-27 16:45 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed SortingAlgorithms ─────────── v0.3.1
Installed Tables ────────────────────── v0.2.11
Installed Compat ────────────────────── v2.2.0
Installed Parsers ───────────────────── v0.3.10
Installed FilePathsBase ─────────────── v0.7.0
Installed OrderedCollections ────────── v1.1.0
Installed DeIdentification ──────────── v0.8.0
Installed Syslogs ───────────────────── v0.3.0
Installed WeakRefStrings ────────────── v0.6.2
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed DataValueInterfaces ───────── v1.0.0
Installed Glob ──────────────────────── v1.2.0
Installed Zlib_jll ──────────────────── v1.2.11+7
Installed Missings ──────────────────── v0.4.3
Installed DataStructures ────────────── v0.17.9
Installed JSON ──────────────────────── v0.21.0
Installed Libiconv_jll ──────────────── v1.16.0+0
Installed Mocking ───────────────────── v0.7.0
Installed YAML ──────────────────────── v0.3.2
Installed TableTraits ───────────────── v1.0.0
Installed PooledArrays ──────────────── v0.5.3
Installed CategoricalArrays ─────────── v0.7.7
Installed DataAPI ───────────────────── v1.1.0
Installed EzXML ─────────────────────── v1.1.0
Installed DataFrames ────────────────── v0.20.0
Installed InvertedIndices ───────────── v1.0.0
Installed XML2_jll ──────────────────── v2.9.9+1
Installed Reexport ──────────────────── v0.2.0
Installed Codecs ────────────────────── v0.5.0
Installed CSV ───────────────────────── v0.5.22
Installed Memento ───────────────────── v0.12.1
Installed TimeZones ─────────────────── v0.11.0
Updating `~/.julia/environments/v1.5/Project.toml`
[b905b068] + DeIdentification v0.8.0
Updating `~/.julia/environments/v1.5/Manifest.toml`
[336ed68f] + CSV v0.5.22
[324d7699] + CategoricalArrays v0.7.7
[19ecbf4d] + Codecs v0.5.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.20.0
[864edb3b] + DataStructures v0.17.9
[e2d170a0] + DataValueInterfaces v1.0.0
[b905b068] + DeIdentification v0.8.0
[8f5d6c58] + EzXML v1.1.0
[48062228] + FilePathsBase v0.7.0
[c27321d9] + Glob v1.2.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[94ce4f54] + Libiconv_jll v1.16.0+0
[f28f55f0] + Memento v0.12.1
[e1d29d7a] + Missings v0.4.3
[78c3b35d] + Mocking v0.7.0
[bac558e1] + OrderedCollections v1.1.0
[69de0a69] + Parsers v0.3.10
[2dfb63ee] + PooledArrays v0.5.3
[189a3867] + Reexport v0.2.0
[a2af1166] + SortingAlgorithms v0.3.1
[cea106d9] + Syslogs v0.3.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[f269a46b] + TimeZones v0.11.0
[ea10d353] + WeakRefStrings v0.6.2
[02c8fc9c] + XML2_jll v2.9.9+1
[ddb6d928] + YAML v0.3.2
[83775a58] + Zlib_jll v1.2.11+7
[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
Building TimeZones → `~/.julia/packages/TimeZones/HAL5Z/deps/build.log`
Updating `/tmp/jl_0Ne6uI/Project.toml`
[no changes]
Updating `/tmp/jl_0Ne6uI/Manifest.toml`
[no changes]
Testing DeIdentification
Updating `/tmp/jl_j46G97/Project.toml`
[no changes]
Updating `/tmp/jl_j46G97/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_j46G97/Project.toml`
[336ed68f] CSV v0.5.22
[a93c6f00] DataFrames v0.20.0
[864edb3b] DataStructures v0.17.9
[b905b068] DeIdentification v0.8.0
[c27321d9] Glob v1.2.0
[682c06a0] JSON v0.21.0
[f28f55f0] Memento v0.12.1
[69de0a69] Parsers v0.3.10
[bd369af6] Tables v0.2.11
[ddb6d928] YAML v0.3.2
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[8dfed614] Test
Test Summary: | Pass Total
config creation | 3 3
Test Summary: | Pass Total
create config from csv | 2 2
Test Summary: | Pass Total
rid generation | 2 2
[info | deidentify]: 2020-01-28T02:57:31.458 Logging session for project ehr
[info | deidentify]: 2020-01-28T02:57:32.034 Setting seed for project ehr
[info | deidentify]: 2020-01-28T02:57:32.034 ====================== Processing dx ======================
[info | deidentify]: 2020-01-28T02:57:32.034 Reading data from ./data/dx.csv
[info | deidentify]: 2020-01-28T02:57:44.295 Renaming file columns
[info | deidentify]: 2020-01-28T02:57:44.349 Checking for primary column
[info | deidentify]: 2020-01-28T02:57:45.456 ====================== Processing dx_custom_dates ======================
[info | deidentify]: 2020-01-28T02:57:45.457 Reading data from ./data/dx_different_date_format.csv
[info | deidentify]: 2020-01-28T02:57:53.384 Renaming file columns
[info | deidentify]: 2020-01-28T02:57:53.384 Checking for primary column
[info | deidentify]: 2020-01-28T02:57:53.393 ====================== Processing dx_messy_dates ======================
[info | deidentify]: 2020-01-28T02:57:53.393 Reading data from ./data/dx_messy_dates.csv
[info | deidentify]: 2020-01-28T02:57:53.957 Renaming file columns
[info | deidentify]: 2020-01-28T02:57:53.957 Checking for primary column
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value WIKKA
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
[info | deidentify]: 2020-01-28T02:57:56.25 ====================== Processing pat ======================
[info | deidentify]: 2020-01-28T02:57:56.251 Reading data from ./data/pat.csv
[info | deidentify]: 2020-01-28T02:57:56.264 Renaming file columns
[info | deidentify]: 2020-01-28T02:57:56.264 Checking for primary column
[info | deidentify]: 2020-01-28T02:57:56.49 ====================== Processing med ======================
[info | deidentify]: 2020-01-28T02:57:56.491 Reading data from ./data/med.csv
[info | deidentify]: 2020-01-28T02:57:56.83 Renaming file columns
[info | deidentify]: 2020-01-28T02:57:56.831 Checking for primary column
[info | deidentify]: 2020-01-28T02:57:56.833 Writing ID dictionaries to ./output/id_dicts_20200128025756.json
[info | deidentify]: 2020-01-28T02:57:57.13 Writing dateshift values to ./output/dateshifts_20200128025756.json
[info | deidentify]: 2020-01-28T02:57:57.281 Writing salt values to ./output/salts_20200128025756.json
Test Summary: | Pass Total
integration tests | 15 15
[info | deidentify]: 2020-01-28T02:58:09.44 Logging session for project ehr
[info | deidentify]: 2020-01-28T02:58:09.44 Setting seed for project ehr
[info | deidentify]: 2020-01-28T02:58:09.441 ====================== Processing dx ======================
[info | deidentify]: 2020-01-28T02:58:09.441 Reading data from ./data/dx.csv
[info | deidentify]: 2020-01-28T02:58:09.443 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.443 Checking for primary column
Test Summary: | Pass Total
primary identifiter | 1 1
[info | deidentify]: 2020-01-28T02:58:09.53 Logging session for project ehr
[info | deidentify]: 2020-01-28T02:58:09.53 Setting seed for project ehr
[info | deidentify]: 2020-01-28T02:58:09.531 ====================== Processing dx ======================
[info | deidentify]: 2020-01-28T02:58:09.531 Reading data from ./data/dx.csv
[info | deidentify]: 2020-01-28T02:58:09.533 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.533 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.542 ====================== Processing dx_custom_dates ======================
[info | deidentify]: 2020-01-28T02:58:09.542 Reading data from ./data/dx_different_date_format.csv
[info | deidentify]: 2020-01-28T02:58:09.544 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.544 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.552 ====================== Processing dx_messy_dates ======================
[info | deidentify]: 2020-01-28T02:58:09.553 Reading data from ./data/dx_messy_dates.csv
[info | deidentify]: 2020-01-28T02:58:09.555 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.555 Checking for primary column
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value WIKKA
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
[info | deidentify]: 2020-01-28T02:58:09.569 ====================== Processing pat ======================
[info | deidentify]: 2020-01-28T02:58:09.569 Reading data from ./data/pat.csv
[info | deidentify]: 2020-01-28T02:58:09.571 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.571 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.66 ====================== Processing med ======================
[info | deidentify]: 2020-01-28T02:58:09.66 Reading data from ./data/med.csv
[info | deidentify]: 2020-01-28T02:58:09.662 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.662 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.666 Writing ID dictionaries to ./output/id_dicts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.666 Writing dateshift values to ./output/dateshifts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.666 Writing salt values to ./output/salts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.667 Logging session for project ehr
[info | deidentify]: 2020-01-28T02:58:09.667 Setting seed for project ehr
[info | deidentify]: 2020-01-28T02:58:09.667 ====================== Processing dx ======================
[info | deidentify]: 2020-01-28T02:58:09.668 Reading data from ./data/dx.csv
[info | deidentify]: 2020-01-28T02:58:09.67 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.67 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.681 ====================== Processing dx_custom_dates ======================
[info | deidentify]: 2020-01-28T02:58:09.681 Reading data from ./data/dx_different_date_format.csv
[info | deidentify]: 2020-01-28T02:58:09.683 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.684 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.693 ====================== Processing dx_messy_dates ======================
[info | deidentify]: 2020-01-28T02:58:09.693 Reading data from ./data/dx_messy_dates.csv
[info | deidentify]: 2020-01-28T02:58:09.696 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.697 Checking for primary column
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value NULL
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
┌ Warning: Could not date shift non-date value WIKKA
└ @ DeIdentification ~/.julia/packages/DeIdentification/JjCZK/src/de_identify.jl:183
[info | deidentify]: 2020-01-28T02:58:09.71 ====================== Processing pat ======================
[info | deidentify]: 2020-01-28T02:58:09.71 Reading data from ./data/pat.csv
[info | deidentify]: 2020-01-28T02:58:09.712 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.712 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.802 ====================== Processing med ======================
[info | deidentify]: 2020-01-28T02:58:09.803 Reading data from ./data/med.csv
[info | deidentify]: 2020-01-28T02:58:09.804 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.804 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.808 Writing ID dictionaries to ./output/id_dicts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.809 Writing dateshift values to ./output/dateshifts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.809 Writing salt values to ./output/salts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.81 Logging session for project ehr
[info | deidentify]: 2020-01-28T02:58:09.81 Setting seed for project ehr
[info | deidentify]: 2020-01-28T02:58:09.81 ====================== Processing dx ======================
[info | deidentify]: 2020-01-28T02:58:09.81 Reading data from ./data/dx.csv
[info | deidentify]: 2020-01-28T02:58:09.812 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.813 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.822 ====================== Processing pat ======================
[info | deidentify]: 2020-01-28T02:58:09.823 Reading data from ./data/pat.csv
[info | deidentify]: 2020-01-28T02:58:09.825 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.825 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.904 ====================== Processing med ======================
[info | deidentify]: 2020-01-28T02:58:09.905 Reading data from ./data/med.csv
[info | deidentify]: 2020-01-28T02:58:09.906 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:09.906 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:09.91 Writing ID dictionaries to ./output/id_dicts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.91 Writing dateshift values to ./output/dateshifts_20200128025809.json
[info | deidentify]: 2020-01-28T02:58:09.911 Writing salt values to ./output/salts_20200128025809.json
Test Summary: | Pass Total
hash seeding | 2 2
[info | deidentify]: 2020-01-28T02:58:10.007 Logging session for project ehr
[info | deidentify]: 2020-01-28T02:58:10.008 Setting seed for project ehr
[info | deidentify]: 2020-01-28T02:58:10.008 ====================== Processing dx ======================
[info | deidentify]: 2020-01-28T02:58:10.008 Reading data from ./data/dx.csv
[info | deidentify]: 2020-01-28T02:58:10.01 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:10.01 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:10.02 ====================== Processing pat ======================
[info | deidentify]: 2020-01-28T02:58:10.02 Reading data from ./data/pat.csv
[info | deidentify]: 2020-01-28T02:58:10.022 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:10.022 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:10.11 ====================== Processing med ======================
[info | deidentify]: 2020-01-28T02:58:10.11 Reading data from ./data/med.csv
[info | deidentify]: 2020-01-28T02:58:10.111 Renaming file columns
[info | deidentify]: 2020-01-28T02:58:10.112 Checking for primary column
[info | deidentify]: 2020-01-28T02:58:10.115 Writing ID dictionaries to ./path/to/new/output/id_dicts_20200128025810.json
[info | deidentify]: 2020-01-28T02:58:10.116 Writing dateshift values to ./path/to/new/output/dateshifts_20200128025810.json
[info | deidentify]: 2020-01-28T02:58:10.117 Writing salt values to ./path/to/new/output/salts_20200128025810.json
Test Summary: | Pass Total
create output directories | 2 2
Testing DeIdentification tests passed