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1.4.0-DEV-082f446f52.log
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Julia Version 1.4.0-DEV.674
Commit 082f446f52 (2020-01-02 16:59 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-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
Resolving package versions...
Installed PooledArrays ──────────────── v0.5.3
Installed Zlib_jll ──────────────────── v1.2.11+7
Installed DataAPI ───────────────────── v1.1.0
Installed Rmath ─────────────────────── v0.6.0
Installed Parsers ───────────────────── v0.3.10
Installed XLSX ──────────────────────── v0.5.8
Installed GigaSOM ───────────────────── v0.2.2
Installed DataFrames ────────────────── v0.19.4
Installed DataValueInterfaces ───────── v1.0.0
Installed InvertedIndices ───────────── v1.0.0
Installed Distances ─────────────────── v0.8.2
Installed SpecialFunctions ──────────── v0.9.0
Installed SortingAlgorithms ─────────── v0.3.1
Installed OpenBLAS_jll ──────────────── v0.3.7+2
Installed FillArrays ────────────────── v0.8.2
Installed StatsFuns ─────────────────── v0.9.3
Installed Compat ────────────────────── v2.2.0
Installed FilePathsBase ─────────────── v0.7.0
Installed BinaryProvider ────────────── v0.5.8
Installed WeakRefStrings ────────────── v0.6.2
Installed QuadGK ────────────────────── v2.3.1
Installed Arpack ────────────────────── v0.4.0
Installed ZipFile ───────────────────── v0.9.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed OrderedCollections ────────── v1.1.0
Installed EzXML ─────────────────────── v0.9.5
Installed Arpack_jll ────────────────── v3.5.0+2
Installed PDMats ────────────────────── v0.9.10
Installed Reexport ──────────────────── v0.2.0
Installed Distributions ─────────────── v0.21.11
Installed DistributedArrays ─────────── v0.6.4
Installed Missings ──────────────────── v0.4.3
Installed CategoricalArrays ─────────── v0.7.5
Installed Primes ────────────────────── v0.4.0
Installed StatsBase ─────────────────── v0.32.0
Installed Tables ────────────────────── v0.2.11
Installed NearestNeighbors ──────────── v0.4.4
Installed DataStructures ────────────── v0.17.6
Installed TableTraits ───────────────── v1.0.0
Installed JSON ──────────────────────── v0.21.0
Installed FileIO ────────────────────── v1.2.1
Installed FCSFiles ──────────────────── v0.1.1
Installed StaticArrays ──────────────── v0.12.1
Installed CSV ───────────────────────── v0.5.21
Updating `~/.julia/environments/v1.4/Project.toml`
[a03a9c34] + GigaSOM v0.2.2
Updating `~/.julia/environments/v1.4/Manifest.toml`
[7d9fca2a] + Arpack v0.4.0
[68821587] + Arpack_jll v3.5.0+2
[b99e7846] + BinaryProvider v0.5.8
[336ed68f] + CSV v0.5.21
[324d7699] + CategoricalArrays v0.7.5
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.19.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[b4f34e82] + Distances v0.8.2
[aaf54ef3] + DistributedArrays v0.6.4
[31c24e10] + Distributions v0.21.11
[8f5d6c58] + EzXML v0.9.5
[d76558cf] + FCSFiles v0.1.1
[5789e2e9] + FileIO v1.2.1
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[a03a9c34] + GigaSOM v0.2.2
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[e1d29d7a] + Missings v0.4.3
[b8a86587] + NearestNeighbors v0.4.4
[4536629a] + OpenBLAS_jll v0.3.7+2
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[69de0a69] + Parsers v0.3.10
[2dfb63ee] + PooledArrays v0.5.3
[27ebfcd6] + Primes v0.4.0
[1fd47b50] + QuadGK v2.3.1
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.3
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[ea10d353] + WeakRefStrings v0.6.2
[fdbf4ff8] + XLSX v0.5.8
[a5390f91] + ZipFile v0.9.0
[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
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Rmath → `~/.julia/packages/Rmath/BoBag/deps/build.log`
Updating `/tmp/jl_31vETU/Project.toml`
[no changes]
Updating `/tmp/jl_31vETU/Manifest.toml`
[no changes]
Building EzXML → `~/.julia/packages/EzXML/QtGgF/deps/build.log`
Updating `/tmp/jl_GjSd4s/Project.toml`
[no changes]
Updating `/tmp/jl_GjSd4s/Manifest.toml`
[no changes]
Testing GigaSOM
Updating `/tmp/jl_xtbIir/Project.toml`
[no changes]
Updating `/tmp/jl_xtbIir/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_xtbIir/Project.toml`
[336ed68f] CSV v0.5.21
[a93c6f00] DataFrames v0.19.4
[b4f34e82] Distances v0.8.2
[aaf54ef3] DistributedArrays v0.6.4
[31c24e10] Distributions v0.21.11
[d76558cf] FCSFiles v0.1.1
[5789e2e9] FileIO v1.2.1
[a03a9c34] GigaSOM v0.2.2
[682c06a0] JSON v0.21.0
[b8a86587] NearestNeighbors v0.4.4
[fdbf4ff8] XLSX v0.5.8
[8ba89e20] Distributed
[9a3f8284] Random
[ea8e919c] SHA
[8dfed614] Test
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
[ Info: The radius has been determined automatically.
Radius: 7.0710678118654755
Batch: Test Failed at /home/pkgeval/.julia/packages/GigaSOM/IPIOH/test/batch.jl:55
Expression: refBatchDfCodes == batchDfCodesTest
Evaluated: 10×10 DataFrame. Omitted printing of 4 columns
│ Row │ CD3 │ CD45 │ CD4 │ CD20 │ CD33 │ CD123 │
│ │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │
├─────┼─────────┼─────────┼─────────┼──────────┼──────────┼───────────┤
│ 1 │ 2.17562 │ 5.06073 │ 1.52296 │ 0.411481 │ 0.123321 │ 0.0552946 │
│ 2 │ 2.15522 │ 5.105 │ 1.51267 │ 0.388815 │ 0.158346 │ 0.100901 │
│ 3 │ 2.10844 │ 5.14377 │ 1.53902 │ 0.381674 │ 0.209516 │ 0.175111 │
│ 4 │ 2.04786 │ 5.17307 │ 1.60862 │ 0.400285 │ 0.269093 │ 0.269429 │
│ 5 │ 2.00096 │ 5.19129 │ 1.71735 │ 0.448452 │ 0.321568 │ 0.359893 │
│ 6 │ 1.99631 │ 5.20022 │ 1.84891 │ 0.517993 │ 0.352834 │ 0.418327 │
│ 7 │ 2.04444 │ 5.20353 │ 1.98118 │ 0.59147 │ 0.36037 │ 0.430147 │
│ 8 │ 2.13286 │ 5.20444 │ 2.0951 │ 0.651107 │ 0.353311 │ 0.400351 │
│ 9 │ 2.23729 │ 5.20471 │ 2.18 │ 0.68602 │ 0.344025 │ 0.345042 │
│ 10 │ 2.33559 │ 5.20507 │ 2.23443 │ 0.694313 │ 0.340601 │ 0.280396 │ == 10×10 DataFrame. Omitted printing of 4 columns
│ Row │ CD3 │ CD45 │ CD4 │ CD20 │ CD33 │ CD123 │
│ │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │
├─────┼─────────┼─────────┼─────────┼──────────┼──────────┼───────────┤
│ 1 │ 2.17562 │ 5.06073 │ 1.52296 │ 0.411481 │ 0.123321 │ 0.0552946 │
│ 2 │ 2.15522 │ 5.105 │ 1.51267 │ 0.388815 │ 0.158346 │ 0.100901 │
│ 3 │ 2.10844 │ 5.14377 │ 1.53902 │ 0.381674 │ 0.209516 │ 0.175111 │
│ 4 │ 2.04786 │ 5.17307 │ 1.60862 │ 0.400285 │ 0.269093 │ 0.269429 │
│ 5 │ 2.00096 │ 5.19129 │ 1.71735 │ 0.448452 │ 0.321568 │ 0.359893 │
│ 6 │ 1.99631 │ 5.20022 │ 1.84891 │ 0.517993 │ 0.352834 │ 0.418327 │
│ 7 │ 2.04444 │ 5.20353 │ 1.98118 │ 0.59147 │ 0.36037 │ 0.430147 │
│ 8 │ 2.13286 │ 5.20444 │ 2.0951 │ 0.651107 │ 0.353311 │ 0.400351 │
│ 9 │ 2.23729 │ 5.20471 │ 2.18 │ 0.68602 │ 0.344025 │ 0.345042 │
│ 10 │ 2.33559 │ 5.20507 │ 2.23443 │ 0.694313 │ 0.340601 │ 0.280396 │
Stacktrace:
[1] macro expansion at /home/pkgeval/.julia/packages/GigaSOM/IPIOH/test/batch.jl:55 [inlined]
[2] macro expansion at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Test/src/Test.jl:1116 [inlined]
[3] top-level scope at /home/pkgeval/.julia/packages/GigaSOM/IPIOH/test/batch.jl:30
Radius: 6.0
Radius: 0.1
Test Summary: | Pass Fail Total
GigaSOM test suite | 44 1 45
Sort and reduce test | 3 3
Checksums | 1 1
Dimensions - batch | 4 4
Batch | 13 1 14
Dimensions - parallel | 4 4
Parallel | 14 14
Test Satellite Functions | 5 5
ERROR: LoadError: Some tests did not pass: 44 passed, 1 failed, 0 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/GigaSOM/IPIOH/test/runtests.jl:8
err = ProcessFailedException(Base.Process[Process(`/opt/julia/bin/julia -Cnative -J/opt/julia/lib/julia/sys.so -g1 --code-coverage=none --color=no --compiled-modules=yes --check-bounds=yes --inline=yes --startup-file=no --track-allocation=none --eval 'append!(empty!(Base.DEPOT_PATH), ["/home/pkgeval/.julia", "/opt/julia/local/share/julia", "/opt/julia/share/julia", "/usr/local/share/julia"])
append!(empty!(Base.DL_LOAD_PATH), String[])
cd("/home/pkgeval/.julia/packages/GigaSOM/IPIOH/test")
append!(empty!(ARGS), String[])
include("/home/pkgeval/.julia/packages/GigaSOM/IPIOH/test/runtests.jl")
'`, ProcessExited(1))])
ERROR: Package GigaSOM errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/Types.jl:54
[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/v1.4/Pkg/src/Operations.jl:1471
[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/v1.4/Pkg/src/API.jl:313
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:300
[5] #test#66 at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:294 [inlined]
[6] test at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:294 [inlined]
[7] #test#65 at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:293 [inlined]
[8] test at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:293 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:292
[10] test(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:292
[11] top-level scope at none:12