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1.6.0-DEV-03e1a89ff1.log
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Julia Version 1.6.0-DEV.633
Commit 03e1a89ff1 (2020-08-13 14:37 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-9.0.1 (ORCJIT, skylake-avx512)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
[ Info: LEGAL NOTICE: package operations send anonymous data about your system to https://pkg.julialang.org (your current package server), including the operating system and Julia versions you are using, and a random client UUID. Running `Pkg.telemetryinfo()` will show exactly what data is sent. See https://julialang.org/legal/data/ for more details about what this data is used for, how long it is retained, and how to opt out of sending it.
Installed Rmath ──────────────────────── v0.6.1
Installed InvertedIndices ────────────── v1.0.0
Installed IteratorInterfaceExtensions ── v1.0.0
Installed PDMats ─────────────────────── v0.10.0
Installed SentinelArrays ─────────────── v1.2.10
Installed Parsers ────────────────────── v1.0.10
Installed DataFrames ─────────────────── v0.21.6
Installed GigaSOM ────────────────────── v0.5.1
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed Rmath_jll ──────────────────── v0.2.2+1
Installed DataAPI ────────────────────── v1.3.0
Installed FillArrays ─────────────────── v0.9.2
Installed StatsFuns ──────────────────── v0.9.5
Installed DistributedArrays ──────────── v0.6.5
Installed OrderedCollections ─────────── v1.3.0
Installed CategoricalArrays ──────────── v0.8.1
Installed DataValueInterfaces ────────── v1.0.0
Installed CompilerSupportLibraries_jll ─ v0.3.3+0
Installed Missings ───────────────────── v0.4.3
Installed ZipFile ────────────────────── v0.9.2
Installed NearestNeighbors ───────────── v0.4.6
Installed SpecialFunctions ───────────── v0.10.3
Installed EzXML ──────────────────────── v1.1.0
Installed StaticArrays ───────────────── v0.12.4
Installed XML2_jll ───────────────────── v2.9.10+1
Installed Reexport ───────────────────── v0.2.0
Installed Compat ─────────────────────── v3.13.0
Installed Primes ─────────────────────── v0.4.0
Installed XLSX ───────────────────────── v0.7.3
Installed Distances ──────────────────── v0.9.0
Installed QuadGK ─────────────────────── v2.4.0
Installed FileIO ─────────────────────── v1.4.1
Installed Tables ─────────────────────── v1.0.5
Installed Zlib_jll ───────────────────── v1.2.11+15
Installed StatsBase ──────────────────── v0.33.0
Installed JSON ───────────────────────── v0.21.0
Installed Distributions ──────────────── v0.23.9
Installed PooledArrays ───────────────── v0.5.3
Installed Libiconv_jll ───────────────── v1.16.0+5
Installed TableTraits ────────────────── v1.0.0
Installed SortingAlgorithms ──────────── v0.3.1
Installed CSV ────────────────────────── v0.7.7
Installed DataStructures ─────────────── v0.17.20
Installed FCSFiles ───────────────────── v0.1.2
Updating `~/.julia/environments/v1.6/Project.toml`
[a03a9c34] + GigaSOM v0.5.1
Updating `~/.julia/environments/v1.6/Manifest.toml`
[336ed68f] + CSV v0.7.7
[324d7699] + CategoricalArrays v0.8.1
[34da2185] + Compat v3.13.0
[e66e0078] + CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] + DataAPI v1.3.0
[a93c6f00] + DataFrames v0.21.6
[864edb3b] + DataStructures v0.17.20
[e2d170a0] + DataValueInterfaces v1.0.0
[b4f34e82] + Distances v0.9.0
[aaf54ef3] + DistributedArrays v0.6.5
[31c24e10] + Distributions v0.23.9
[8f5d6c58] + EzXML v1.1.0
[d76558cf] + FCSFiles v0.1.2
[5789e2e9] + FileIO v1.4.1
[1a297f60] + FillArrays v0.9.2
[a03a9c34] + GigaSOM v0.5.1
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[94ce4f54] + Libiconv_jll v1.16.0+5
[e1d29d7a] + Missings v0.4.3
[b8a86587] + NearestNeighbors v0.4.6
[efe28fd5] + OpenSpecFun_jll v0.5.3+3
[bac558e1] + OrderedCollections v1.3.0
[90014a1f] + PDMats v0.10.0
[69de0a69] + Parsers v1.0.10
[2dfb63ee] + PooledArrays v0.5.3
[27ebfcd6] + Primes v0.4.0
[1fd47b50] + QuadGK v2.4.0
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.1
[f50d1b31] + Rmath_jll v0.2.2+1
[91c51154] + SentinelArrays v1.2.10
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.10.3
[90137ffa] + StaticArrays v0.12.4
[2913bbd2] + StatsBase v0.33.0
[4c63d2b9] + StatsFuns v0.9.5
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v1.0.5
[fdbf4ff8] + XLSX v0.7.3
[02c8fc9c] + XML2_jll v2.9.10+1
[a5390f91] + ZipFile v0.9.2
[83775a58] + Zlib_jll v1.2.11+15
[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
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Testing GigaSOM
Status `/tmp/jl_tFVn3f/Project.toml`
[336ed68f] CSV v0.7.7
[a93c6f00] DataFrames v0.21.6
[b4f34e82] Distances v0.9.0
[aaf54ef3] DistributedArrays v0.6.5
[31c24e10] Distributions v0.23.9
[d76558cf] FCSFiles v0.1.2
[5789e2e9] FileIO v1.4.1
[a03a9c34] GigaSOM v0.5.1
[682c06a0] JSON v0.21.0
[b8a86587] NearestNeighbors v0.4.6
[fdbf4ff8] XLSX v0.7.3
[8ba89e20] Distributed
[37e2e46d] LinearAlgebra
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[8dfed614] Test
Status `/tmp/jl_tFVn3f/Manifest.toml`
[336ed68f] CSV v0.7.7
[324d7699] CategoricalArrays v0.8.1
[34da2185] Compat v3.13.0
[e66e0078] CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] DataAPI v1.3.0
[a93c6f00] DataFrames v0.21.6
[864edb3b] DataStructures v0.17.20
[e2d170a0] DataValueInterfaces v1.0.0
[b4f34e82] Distances v0.9.0
[aaf54ef3] DistributedArrays v0.6.5
[31c24e10] Distributions v0.23.9
[8f5d6c58] EzXML v1.1.0
[d76558cf] FCSFiles v0.1.2
[5789e2e9] FileIO v1.4.1
[1a297f60] FillArrays v0.9.2
[a03a9c34] GigaSOM v0.5.1
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.0
[94ce4f54] Libiconv_jll v1.16.0+5
[e1d29d7a] Missings v0.4.3
[b8a86587] NearestNeighbors v0.4.6
[efe28fd5] OpenSpecFun_jll v0.5.3+3
[bac558e1] OrderedCollections v1.3.0
[90014a1f] PDMats v0.10.0
[69de0a69] Parsers v1.0.10
[2dfb63ee] PooledArrays v0.5.3
[27ebfcd6] Primes v0.4.0
[1fd47b50] QuadGK v2.4.0
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+1
[91c51154] SentinelArrays v1.2.10
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.10.3
[90137ffa] StaticArrays v0.12.4
[2913bbd2] StatsBase v0.33.0
[4c63d2b9] StatsFuns v0.9.5
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v1.0.5
[fdbf4ff8] XLSX v0.7.3
[02c8fc9c] XML2_jll v2.9.10+1
[a5390f91] ZipFile v0.9.2
[83775a58] Zlib_jll v1.2.11+15
[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
[4607b0f0] SuiteSparse
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
Archive: PBMC8_fcs_files.zip
inflating: PBMC8_30min_patient1_BCR-XL.fcs
inflating: PBMC8_30min_patient1_Reference.fcs
inflating: PBMC8_30min_patient2_BCR-XL.fcs
inflating: PBMC8_30min_patient2_Reference.fcs
inflating: PBMC8_30min_patient3_BCR-XL.fcs
inflating: PBMC8_30min_patient3_Reference.fcs
inflating: PBMC8_30min_patient4_BCR-XL.fcs
inflating: PBMC8_30min_patient4_Reference.fcs
inflating: PBMC8_30min_patient5_BCR-XL.fcs
inflating: PBMC8_30min_patient5_Reference.fcs
inflating: PBMC8_30min_patient6_BCR-XL.fcs
inflating: PBMC8_30min_patient6_Reference.fcs
inflating: PBMC8_30min_patient7_BCR-XL.fcs
inflating: PBMC8_30min_patient7_Reference.fcs
inflating: PBMC8_30min_patient8_BCR-XL.fcs
inflating: PBMC8_30min_patient8_Reference.fcs
Check results: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:52
Expression: refBatchWinners == batchWinnersTest
Evaluated: 10×1 DataFrame
│ Row │ index │
│ │ Int64 │
├─────┼───────┤
│ 1 │ 92 │
│ 2 │ 91 │
│ 3 │ 6 │
│ 4 │ 91 │
│ 5 │ 10 │
│ 6 │ 4 │
│ 7 │ 10 │
│ 8 │ 10 │
│ 9 │ 6 │
│ 10 │ 5 │ == 10×1 DataFrame
│ Row │ index │
│ │ Int64 │
├─────┼───────┤
│ 1 │ 100 │
│ 2 │ 100 │
│ 3 │ 81 │
│ 4 │ 1 │
│ 5 │ 91 │
│ 6 │ 10 │
│ 7 │ 10 │
│ 8 │ 91 │
│ 9 │ 9 │
│ 10 │ 10 │
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:52
[2] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[3] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:28
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[5] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:4
Check results: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:53
Expression: ≈(Matrix{Float64}(refBatchDfCodes), Matrix{Float64}(batchDfCodesTest), atol = 0.0001)
Evaluated: [-0.011651251029458529 0.002166440919825469 … 0.008291097574972593 -0.013889722801698756; -0.015951824546522195 -0.002697429870211619 … 0.005161131828402003 -0.011165165902673387; … ; -0.019292562591419423 -0.009278789640504858 … -0.020056421918357603 0.019975333140029673; -0.016247269914707884 -0.00740984542325823 … -0.024373583393098794 0.025644294109764914] ≈ [-0.0043652777347860305 0.011427071378938067 … 0.020191736050801923 -0.00647960180458844; -0.0023562587107531173 0.009433197260491605 … 0.018799891714881493 -0.007597359542517521; … ; 0.005206434593773228 0.007178712253075592 … 0.0036621507302797792 -0.007341699521398385; 0.008818415750503732 0.0060504577642585666 … -0.0005777873647506914 -0.005384032820078919] (atol=0.0001)
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:53
[2] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[3] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:28
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[5] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:4
Check results: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:55
Expression: ≈(Matrix{Float64}(refBatchEmbedded), Matrix{Float64}(batchEmbeddedTest), atol = 0.0001)
Evaluated: [1.5001213674422897 8.880687995083614; 1.2237981567666019 8.782808680684086; … ; 9.15192688427219 0.07446585923210677; 4.115778473902338 0.0563890768039573] ≈ [8.263746847171603 8.551458290785114; 8.192017799548655 8.672926182485256; … ; 8.111052196435553 0.3779425549035254; 8.386191781409218 0.4589190877780119] (atol=0.0001)
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:55
[2] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[3] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:28
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[5] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:4
Check results: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:49
Expression: refParallelWinners == parallelWinnersTest
Evaluated: 10×1 DataFrame
│ Row │ index │
│ │ Int64 │
├─────┼───────┤
│ 1 │ 92 │
│ 2 │ 92 │
│ 3 │ 66 │
│ 4 │ 66 │
│ 5 │ 10 │
│ 6 │ 68 │
│ 7 │ 30 │
│ 8 │ 10 │
│ 9 │ 90 │
│ 10 │ 3 │ == 10×1 DataFrame
│ Row │ index │
│ │ Int64 │
├─────┼───────┤
│ 1 │ 99 │
│ 2 │ 99 │
│ 3 │ 91 │
│ 4 │ 57 │
│ 5 │ 91 │
│ 6 │ 19 │
│ 7 │ 56 │
│ 8 │ 91 │
│ 9 │ 59 │
│ 10 │ 9 │
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:49
[2] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[3] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:24
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[5] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:4
Check results: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:50
Expression: Matrix{Float64}(refParallelDfCodes) ≈ Matrix{Float64}(parallelDfCodesTest)
Evaluated: [-0.17640967142561337 0.4685075475625074 … 0.8104538714781182 -0.998356121477298; -0.7831021091922231 -0.1387601640904325 … 0.5757650485172153 -1.0812869624104249; … ; -1.1410063412612652 -0.541407804316432 … -0.09480486991814785 0.9046371040902668; -0.32086931489919535 0.008572799776121031 … -0.43372445501215534 0.9200262143737115] ≈ [0.25196542103565145 0.6537076297697783 … 1.23034780373161 -0.5560558081682654; -0.15760719273935675 0.40190670508853066 … 1.8131968600871644 -0.862905068543941; … ; -0.8431457565295831 0.1144697601046941 … -0.14115039885763359 -0.8547633857099789; 0.43132077478721836 0.27870645016939544 … -0.49848001894051774 0.07256214274681169]
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:50
[2] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[3] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:24
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[5] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:4
Check results: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:51
Expression: ≈(Matrix{Float64}(refParallelEmbedded), Matrix{Float64}(parallelEmbeddedTest), atol = 0.0001)
Evaluated: [1.6744019997736426 8.103683903608214; 1.7010846112311093 8.401485398046395; … ; 9.029942763218518 4.162009375605646; 2.8330767297731123 2.1536182096362584] ≈ [7.385233967435518 7.539497761736817; 7.887458220619995 6.720890707024089; … ; 6.629316678231864 4.280308179407296; 7.537452567748045 0.9750086039350312] (atol=0.0001)
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:51
[2] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[3] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:24
[4] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1114
[5] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:4
Test Summary: | Pass Fail Total
GigaSOM test suite | 138 6 144
Distributed data handling | 27 27
High-level operations on distributed data | 33 33
SOM training helper functions | 15 15
Dataset splitting helpers | 10 10
File loading with compensation | 1 1
load-time columns normalization | 1 1
Single-CPU batch processing | 6 3 9
Check SOM dimensions | 4 4
Check results | 1 3 4
Parallel processing | 5 3 8
Check SOM dimensions | 4 4
Check results | 1 3 4
File splitting | 40 40
ERROR: LoadError: Some tests did not pass: 138 passed, 6 failed, 0 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/runtests.jl:20
ERROR: Package GigaSOM errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N)
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:52
[2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1567
[3] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:328
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:315
[5] #test#62
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67 [inlined]
[6] test
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67 [inlined]
[7] #test#61
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[8] test
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[9] test(pkg::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[10] test(pkg::String)
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[11] top-level scope
@ none:16