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1.6.0-DEV-22b5d93b2b.log
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Julia Version 1.6.0-DEV.1069
Commit 22b5d93b2b (2020-09-28 17:33 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-10.0.1 (ORCJIT, skylake-avx512)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed Missings ───────────────────── v0.4.4
Installed InvertedIndices ────────────── v1.0.0
Installed Zlib_jll ───────────────────── v1.2.11+16
Installed Primes ─────────────────────── v0.4.0
Installed QuadGK ─────────────────────── v2.4.1
Installed StructTypes ────────────────── v1.1.0
Installed DataStructures ─────────────── v0.18.6
Installed GigaSOM ────────────────────── v0.5.1
Installed Compat ─────────────────────── v3.17.0
Installed Rmath_jll ──────────────────── v0.2.2+1
Installed SortingAlgorithms ──────────── v0.3.1
Installed CompilerSupportLibraries_jll ─ v0.3.3+0
Installed Libiconv_jll ───────────────── v1.16.0+6
Installed EzXML ──────────────────────── v1.1.0
Installed Tables ─────────────────────── v1.0.5
Installed DataValueInterfaces ────────── v1.0.0
Installed CSV ────────────────────────── v0.7.7
Installed Distances ──────────────────── v0.9.0
Installed SentinelArrays ─────────────── v1.2.15
Installed PDMats ─────────────────────── v0.10.1
Installed XLSX ───────────────────────── v0.7.3
Installed FileIO ─────────────────────── v1.4.3
Installed Distributions ──────────────── v0.23.12
Installed PooledArrays ───────────────── v0.5.3
Installed DistributedArrays ──────────── v0.6.5
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed TableTraits ────────────────── v1.0.0
Installed Parsers ────────────────────── v1.0.10
Installed OrderedCollections ─────────── v1.3.1
Installed SpecialFunctions ───────────── v0.10.3
Installed NearestNeighbors ───────────── v0.4.6
Installed XML2_jll ───────────────────── v2.9.10+2
Installed DataAPI ────────────────────── v1.3.0
Installed Reexport ───────────────────── v0.2.0
Installed JSON ───────────────────────── v0.21.1
Installed StaticArrays ───────────────── v0.12.4
Installed CategoricalArrays ──────────── v0.8.3
Installed StatsFuns ──────────────────── v0.9.5
Installed StatsBase ──────────────────── v0.33.1
Installed FCSFiles ───────────────────── v0.1.2
Installed FillArrays ─────────────────── v0.9.6
Installed DataFrames ─────────────────── v0.21.7
Installed ZipFile ────────────────────── v0.9.2
Installed Rmath ──────────────────────── v0.6.1
Installed IteratorInterfaceExtensions ── v1.0.0
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 v0.8.3
[34da2185] + Compat v3.17.0
[e66e0078] + CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] + DataAPI v1.3.0
[a93c6f00] + DataFrames v0.21.7
[864edb3b] + DataStructures v0.18.6
[e2d170a0] + DataValueInterfaces v1.0.0
[b4f34e82] + Distances v0.9.0
[aaf54ef3] + DistributedArrays v0.6.5
[31c24e10] + Distributions v0.23.12
[8f5d6c58] + EzXML v1.1.0
[d76558cf] + FCSFiles v0.1.2
[5789e2e9] + FileIO v1.4.3
[1a297f60] + FillArrays v0.9.6
[a03a9c34] + GigaSOM v0.5.1
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.1
[94ce4f54] + Libiconv_jll v1.16.0+6
[e1d29d7a] + Missings v0.4.4
[b8a86587] + NearestNeighbors v0.4.6
[efe28fd5] + OpenSpecFun_jll v0.5.3+3
[bac558e1] + OrderedCollections v1.3.1
[90014a1f] + PDMats v0.10.1
[69de0a69] + Parsers v1.0.10
[2dfb63ee] + PooledArrays v0.5.3
[27ebfcd6] + Primes v0.4.0
[1fd47b50] + QuadGK v2.4.1
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.1
[f50d1b31] + Rmath_jll v0.2.2+1
[91c51154] + SentinelArrays v1.2.15
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.10.3
[90137ffa] + StaticArrays v0.12.4
[2913bbd2] + StatsBase v0.33.1
[4c63d2b9] + StatsFuns v0.9.5
[856f2bd8] + StructTypes v1.1.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v1.0.5
[fdbf4ff8] + XLSX v0.7.3
[02c8fc9c] + XML2_jll v2.9.10+2
[a5390f91] + ZipFile v0.9.2
[83775a58] + Zlib_jll v1.2.11+16
[56f22d72] + Artifacts
[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
[fa267f1f] + TOML
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Testing GigaSOM
Status `/tmp/jl_9uOBeG/Project.toml`
[336ed68f] CSV v0.7.7
[a93c6f00] DataFrames v0.21.7
[b4f34e82] Distances v0.9.0
[aaf54ef3] DistributedArrays v0.6.5
[31c24e10] Distributions v0.23.12
[d76558cf] FCSFiles v0.1.2
[5789e2e9] FileIO v1.4.3
[a03a9c34] GigaSOM v0.5.1
[682c06a0] JSON v0.21.1
[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_9uOBeG/Manifest.toml`
[336ed68f] CSV v0.7.7
[324d7699] CategoricalArrays v0.8.3
[34da2185] Compat v3.17.0
[e66e0078] CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] DataAPI v1.3.0
[a93c6f00] DataFrames v0.21.7
[864edb3b] DataStructures v0.18.6
[e2d170a0] DataValueInterfaces v1.0.0
[b4f34e82] Distances v0.9.0
[aaf54ef3] DistributedArrays v0.6.5
[31c24e10] Distributions v0.23.12
[8f5d6c58] EzXML v1.1.0
[d76558cf] FCSFiles v0.1.2
[5789e2e9] FileIO v1.4.3
[1a297f60] FillArrays v0.9.6
[a03a9c34] GigaSOM v0.5.1
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.1
[94ce4f54] Libiconv_jll v1.16.0+6
[e1d29d7a] Missings v0.4.4
[b8a86587] NearestNeighbors v0.4.6
[efe28fd5] OpenSpecFun_jll v0.5.3+3
[bac558e1] OrderedCollections v1.3.1
[90014a1f] PDMats v0.10.1
[69de0a69] Parsers v1.0.10
[2dfb63ee] PooledArrays v0.5.3
[27ebfcd6] Primes v0.4.0
[1fd47b50] QuadGK v2.4.1
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+1
[91c51154] SentinelArrays v1.2.15
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.10.3
[90137ffa] StaticArrays v0.12.4
[2913bbd2] StatsBase v0.33.1
[4c63d2b9] StatsFuns v0.9.5
[856f2bd8] StructTypes v1.1.0
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v1.0.5
[fdbf4ff8] XLSX v0.7.3
[02c8fc9c] XML2_jll v2.9.10+2
[a5390f91] ZipFile v0.9.2
[83775a58] Zlib_jll v1.2.11+16
[56f22d72] Artifacts
[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
[fa267f1f] TOML
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
Testing Running tests...
┌ Warning: Base.download is deprecated; use Downloads.download instead
│ caller = top-level scope at testLoadPBMC8.jl:33
└ @ Core ~/.julia/packages/GigaSOM/QfzjJ/test/testLoadPBMC8.jl:33
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: Error During Test at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:27
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:39
[10] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[11] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:28
[12] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[13] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testBatch.jl:4
[14] include(fname::String)
@ Base.MainInclude ./client.jl:444
[15] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/runtests.jl:30
[16] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[17] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/runtests.jl:21
[18] include(fname::String)
@ Base.MainInclude ./client.jl:444
[19] top-level scope
@ none:6
[20] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[21] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[22] _start()
@ Base ./client.jl:485
Check results: Error During Test at /home/pkgeval/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:23
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:35
[10] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[11] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:24
[12] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[13] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/testParallel.jl:4
[14] include(fname::String)
@ Base.MainInclude ./client.jl:444
[15] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/runtests.jl:31
[16] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[17] top-level scope
@ ~/.julia/packages/GigaSOM/QfzjJ/test/runtests.jl:21
[18] include(fname::String)
@ Base.MainInclude ./client.jl:444
[19] top-level scope
@ none:6
[20] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[21] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[22] _start()
@ Base ./client.jl:485
Test Summary: | Pass Error Total
GigaSOM test suite | 138 2 140
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 1 7
Check SOM dimensions | 4 4
Check results | 1 1 2
Parallel processing | 5 1 6
Check SOM dimensions | 4 4
Check results | 1 1 2
File splitting | 40 40
ERROR: LoadError: Some tests did not pass: 138 passed, 0 failed, 2 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(msg::String)
@ Pkg.Types /workspace/srcdir/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 /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1609
[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 /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:331
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:318
[5] #test#62
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[6] test
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[7] #test#61
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[8] test
@ /workspace/srcdir/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 /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[10] test(pkg::String)
@ Pkg.API /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[11] top-level scope
@ none:19