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1.6.0-DEV-300e34cf74.log
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################################################################################
# PkgEval set-up: 2020-10-30T04:47:46.947
#
Julia Version 1.6.0-DEV.1380
Commit 300e34cf74 (2020-10-30 02:28 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: AMD EPYC 7502 32-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-11.0.0 (ORCJIT, znver2)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_MAX_NUM_PRECOMPILE_FILES = 9223372036854775807
################################################################################
# Installation: 2020-10-30T04:47:48.412
#
Resolving package versions...
Installed Distances ──────────────────── v0.9.2
Installed Conda ──────────────────────── v1.4.1
Installed CompilerSupportLibraries_jll ─ v0.3.4+0
Installed Rmath ──────────────────────── v0.6.1
Installed JLLWrappers ────────────────── v1.1.3
Installed Parsers ────────────────────── v1.0.11
Installed BiobakeryUtils ─────────────── v0.3.3
Installed VersionParsing ─────────────── v1.2.0
Installed Arpack_jll ─────────────────── v3.5.0+3
Installed WinReg ─────────────────────── v0.3.1
Installed MultivariateStats ──────────── v0.7.0
Installed SpecialFunctions ───────────── v0.10.3
Installed JSON ───────────────────────── v0.21.1
Installed OpenBLAS_jll ───────────────── v0.3.10+0
Installed WeakRefStrings ─────────────── v0.6.2
Installed StructTypes ────────────────── v1.1.0
Installed RandomBooleanMatrices ──────── v0.1.1
Installed SpatialEcology ─────────────── v0.9.6
Installed OrderedCollections ─────────── v1.3.1
Installed DataFrames ─────────────────── v0.21.8
Installed StatsFuns ──────────────────── v0.9.5
Installed IteratorInterfaceExtensions ── v1.0.0
Installed RCall ──────────────────────── v0.13.9
Installed RecipesBase ────────────────── v1.1.0
Installed StatsModels ────────────────── v0.6.15
Installed Requires ───────────────────── v1.1.0
Installed CSV ────────────────────────── v0.6.2
Installed CategoricalArrays ──────────── v0.8.3
Installed DataStructures ─────────────── v0.18.8
Installed RandomNumbers ──────────────── v1.4.0
Installed SortingAlgorithms ──────────── v0.3.1
Installed PooledArrays ───────────────── v0.5.3
Installed OpenSpecFun_jll ────────────── v0.5.3+4
Installed ShiftedArrays ──────────────── v1.0.0
Installed InvertedIndices ────────────── v1.0.0
Installed Microbiome ─────────────────── v0.6.4
Installed Reexport ───────────────────── v0.2.0
Installed DataFramesMeta ─────────────── v0.5.1
Installed Rmath_jll ──────────────────── v0.2.2+1
Installed Arpack ─────────────────────── v0.4.0
Installed EcoBase ────────────────────── v0.1.3
Installed FilePathsBase ──────────────── v0.8.0
Installed DataAPI ────────────────────── v1.3.0
Installed Tables ─────────────────────── v1.1.0
Installed Missings ───────────────────── v0.4.4
Installed Compat ─────────────────────── v3.23.0
Installed DataValueInterfaces ────────── v1.0.0
Installed TableTraits ────────────────── v1.0.0
Installed StatsBase ──────────────────── v0.33.2
Updating `~/.julia/environments/v1.6/Project.toml`
[fa5322f5] + BiobakeryUtils v0.3.3
Updating `~/.julia/environments/v1.6/Manifest.toml`
[7d9fca2a] + Arpack v0.4.0
[fa5322f5] + BiobakeryUtils v0.3.3
[336ed68f] + CSV v0.6.2
[324d7699] + CategoricalArrays v0.8.3
[34da2185] + Compat v3.23.0
[8f4d0f93] + Conda v1.4.1
[9a962f9c] + DataAPI v1.3.0
[a93c6f00] + DataFrames v0.21.8
[1313f7d8] + DataFramesMeta v0.5.1
[864edb3b] + DataStructures v0.18.8
[e2d170a0] + DataValueInterfaces v1.0.0
[b4f34e82] + Distances v0.9.2
[a58aae7d] + EcoBase v0.1.3
[48062228] + FilePathsBase v0.8.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.1.3
[682c06a0] + JSON v0.21.1
[3bd8f0ae] + Microbiome v0.6.4
[e1d29d7a] + Missings v0.4.4
[6f286f6a] + MultivariateStats v0.7.0
[bac558e1] + OrderedCollections v1.3.1
[69de0a69] + Parsers v1.0.11
[2dfb63ee] + PooledArrays v0.5.3
[6f49c342] + RCall v0.13.9
[9ae346a0] + RandomBooleanMatrices v0.1.1
[e6cf234a] + RandomNumbers v1.4.0
[3cdcf5f2] + RecipesBase v1.1.0
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v1.1.0
[79098fc4] + Rmath v0.6.1
[1277b4bf] + ShiftedArrays v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[348f2d5d] + SpatialEcology v0.9.6
[276daf66] + SpecialFunctions v0.10.3
[2913bbd2] + StatsBase v0.33.2
[4c63d2b9] + StatsFuns v0.9.5
[3eaba693] + StatsModels v0.6.15
[856f2bd8] + StructTypes v1.1.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v1.1.0
[81def892] + VersionParsing v1.2.0
[ea10d353] + WeakRefStrings v0.6.2
[1b915085] + WinReg v0.3.1
[68821587] + Arpack_jll v3.5.0+3
[e66e0078] + CompilerSupportLibraries_jll v0.3.4+0
[4536629a] + OpenBLAS_jll v0.3.10+0
[efe28fd5] + OpenSpecFun_jll v0.5.3+4
[f50d1b31] + Rmath_jll v0.2.2+1
[0dad84c5] + ArgTools
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[f43a241f] + Downloads
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[b27032c2] + LibCURL
[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
[fa267f1f] + TOML
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[deac9b47] + LibCURL_jll
[14a3606d] + MozillaCACerts_jll
Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/7a58bb32ce5d85f8bf7559aa7c2842f9aecf52fc/build.log`
Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3a0e886953024454e9f489e309568e134dc7e6ed/build.log`
################################################################################
# Testing: 2020-10-30T04:49:18.175
#
Testing BiobakeryUtils
Status `/tmp/jl_iDPQY3/Project.toml`
[fa5322f5] BiobakeryUtils v0.3.3
[336ed68f] CSV v0.6.2
[a93c6f00] DataFrames v0.21.8
[3bd8f0ae] Microbiome v0.6.4
[6f49c342] RCall v0.13.9
[9a3f8284] Random
[10745b16] Statistics
[8dfed614] Test
Status `/tmp/jl_iDPQY3/Manifest.toml`
[7d9fca2a] Arpack v0.4.0
[fa5322f5] BiobakeryUtils v0.3.3
[336ed68f] CSV v0.6.2
[324d7699] CategoricalArrays v0.8.3
[34da2185] Compat v3.23.0
[8f4d0f93] Conda v1.4.1
[9a962f9c] DataAPI v1.3.0
[a93c6f00] DataFrames v0.21.8
[1313f7d8] DataFramesMeta v0.5.1
[864edb3b] DataStructures v0.18.8
[e2d170a0] DataValueInterfaces v1.0.0
[b4f34e82] Distances v0.9.2
[a58aae7d] EcoBase v0.1.3
[48062228] FilePathsBase v0.8.0
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[692b3bcd] JLLWrappers v1.1.3
[682c06a0] JSON v0.21.1
[3bd8f0ae] Microbiome v0.6.4
[e1d29d7a] Missings v0.4.4
[6f286f6a] MultivariateStats v0.7.0
[bac558e1] OrderedCollections v1.3.1
[69de0a69] Parsers v1.0.11
[2dfb63ee] PooledArrays v0.5.3
[6f49c342] RCall v0.13.9
[9ae346a0] RandomBooleanMatrices v0.1.1
[e6cf234a] RandomNumbers v1.4.0
[3cdcf5f2] RecipesBase v1.1.0
[189a3867] Reexport v0.2.0
[ae029012] Requires v1.1.0
[79098fc4] Rmath v0.6.1
[1277b4bf] ShiftedArrays v1.0.0
[a2af1166] SortingAlgorithms v0.3.1
[348f2d5d] SpatialEcology v0.9.6
[276daf66] SpecialFunctions v0.10.3
[2913bbd2] StatsBase v0.33.2
[4c63d2b9] StatsFuns v0.9.5
[3eaba693] StatsModels v0.6.15
[856f2bd8] StructTypes v1.1.0
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v1.1.0
[81def892] VersionParsing v1.2.0
[ea10d353] WeakRefStrings v0.6.2
[1b915085] WinReg v0.3.1
[68821587] Arpack_jll v3.5.0+3
[e66e0078] CompilerSupportLibraries_jll v0.3.4+0
[4536629a] OpenBLAS_jll v0.3.10+0
[efe28fd5] OpenSpecFun_jll v0.5.3+4
[f50d1b31] Rmath_jll v0.2.2+1
[0dad84c5] ArgTools
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[f43a241f] Downloads
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[b27032c2] LibCURL
[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
[fa267f1f] TOML
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[deac9b47] LibCURL_jll
[14a3606d] MozillaCACerts_jll
Testing Running tests...
┌ Info: Importing abundance table
└ file = "metaphlan_test.tsv"
Biobakery Utilities: Error During Test at /home/pkgeval/.julia/packages/BiobakeryUtils/OO1A3/test/runtests.jl:7
Got exception outside of a @test
REvalError: Error in library(vegan) : there is no package called 'vegan'
Test Summary: | Pass Error Total
Biobakery Utilities | 8 1 9
ERROR: LoadError: Some tests did not pass: 8 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/BiobakeryUtils/OO1A3/test/runtests.jl:7
PkgEval failed: Package BiobakeryUtils 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:1651
[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:334
[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:321
[5] #test#62
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:71 [inlined]
[6] test
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:70 [inlined]
[7] #test#61
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[8] test
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [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:67
[10] test(pkg::String)
@ Pkg.API /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67
[11] top-level scope
@ none:44
[12] eval
@ ./boot.jl:360 [inlined]
[13] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[14] top-level scope
@ none:1
[15] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[16] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[17] _start()
@ Base ./client.jl:485
################################################################################
# PkgEval teardown: 2020-10-30T04:50:46.518
CPU usage: 177.08s (161.81s user, 15.65s kernel)
Network usage:
- eth0: 258.059 MiB received, 1.048 MiB sent
Raw statistics: {"blkio_stats":{"io_queue_recursive":[],"io_serviced_recursive":[{"major":259,"value":0,"op":"Read","minor":0},{"major":259,"value":23,"op":"Write","minor":0},{"major":259,"value":0,"op":"Sync","minor":0},{"major":259,"value":23,"op":"Async","minor":0},{"major":259,"value":23,"op":"Total","minor":0},{"major":253,"value":0,"op":"Read","minor":2},{"major":253,"value":23,"op":"Write","minor":2},{"major":253,"value":0,"op":"Sync","minor":2},{"major":253,"value":23,"op":"Async","minor":2},{"major":253,"value":23,"op":"Total","minor":2}],"io_time_recursive":[],"sectors_recursive":[],"io_service_bytes_recursive":[{"major":259,"value":0,"op":"Read","minor":0},{"major":259,"value":421888,"op":"Write","minor":0},{"major":259,"value":0,"op":"Sync","minor":0},{"major":259,"value":421888,"op":"Async","minor":0},{"major":259,"value":421888,"op":"Total","minor":0},{"major":253,"value":0,"op":"Read","minor":2},{"major":253,"value":421888,"op":"Write","minor":2},{"major":253,"value":0,"op":"Sync","minor":2},{"major":253,"value":421888,"op":"Async","minor":2},{"major":253,"value":421888,"op":"Total","minor":2}],"io_wait_time_recursive":[],"io_merged_recursive":[],"io_service_time_recursive":[]},"memory_stats":{"usage":1782845440,"max_usage":2853826560,"stats":{"hierarchical_memory_limit":9223372036854771712,"pgmajfault":0,"total_rss":256274432,"inactive_file":8192,"inactive_anon":985751552,"total_pgfault":4081380,"total_cache":1482932224,"total_rss_huge":0,"total_active_anon":752685056,"total_pgmajfault":0,"pgpgin":3082876,"rss_huge":0,"mapped_file":0,"total_inactive_file":8192,"dirty":0,"total_unevictable":0,"total_dirty":0,"writeback":0,"pgpgout":2658265,"hierarchical_memsw_limit":0,"cache":1482932224,"active_file":761856,"pgfault":4081380,"total_mapped_file":0,"total_pgpgout":2658265,"total_writeback":0,"rss":256274432,"unevictable":0,"total_inactive_anon":985751552,"total_pgpgin":3082876,"active_anon":752685056,"total_active_file":761856},"limit":540972998656},"name":"/BiobakeryUtils-TVDOeVxz","networks":{"eth0":{"rx_bytes":270594244,"rx_packets":28726,"tx_packets":17785,"tx_bytes":1098687,"tx_dropped":0,"rx_dropped":6,"tx_errors":0,"rx_errors":0}},"id":"b217bc67abc2faba7ee4187ccbc76a2b9234cceef204377b8ff02bf6f461a653","preread":"0001-01-01T00:00:00Z","storage_stats":{},"precpu_stats":{"throttling_data":{"throttled_periods":0,"throttled_time":0,"periods":0},"cpu_usage":{"usage_in_usermode":0,"usage_in_kernelmode":0,"total_usage":0}},"pids_stats":{"current":38},"num_procs":0,"cpu_stats":{"throttling_data":{"throttled_periods":0,"throttled_time":0,"periods":0},"system_cpu_usage":113029397610000000,"online_cpus":128,"cpu_usage":{"usage_in_usermode":161810000000,"usage_in_kernelmode":15650000000,"total_usage":177082837352,"percpu_usage":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,177074277697,8559655,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]}},"read":"2020-10-30T04:50:47.182804778Z"}