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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 InvertedIndices ────────────── v1.0.0
Installed Compat ─────────────────────── v3.17.0
Installed ProgressMeter ──────────────── v1.4.0
Installed Missings ───────────────────── v0.4.4
Installed QuadGK ─────────────────────── v2.4.1
Installed StructTypes ────────────────── v1.1.0
Installed DataStructures ─────────────── v0.18.6
Installed JWAS ───────────────────────── v0.9.0
Installed SortingAlgorithms ──────────── v0.3.1
Installed CompilerSupportLibraries_jll ─ v0.3.3+0
Installed Rmath_jll ──────────────────── v0.2.2+1
Installed WeakRefStrings ─────────────── v0.6.2
Installed PDMats ─────────────────────── v0.10.1
Installed Tables ─────────────────────── v1.0.5
Installed Distributions ──────────────── v0.23.12
Installed DataValueInterfaces ────────── v1.0.0
Installed PooledArrays ───────────────── v0.5.3
Installed TableTraits ────────────────── v1.0.0
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed SpecialFunctions ───────────── v0.10.3
Installed Parsers ────────────────────── v1.0.10
Installed OrderedCollections ─────────── v1.3.1
Installed FilePathsBase ──────────────── v0.8.0
Installed DataAPI ────────────────────── v1.3.0
Installed Reexport ───────────────────── v0.2.0
Installed JSON ───────────────────────── v0.21.1
Installed StatsBase ──────────────────── v0.33.1
Installed StaticArrays ───────────────── v0.12.4
Installed StatsFuns ──────────────────── v0.9.5
Installed CategoricalArrays ──────────── v0.8.3
Installed FillArrays ─────────────────── v0.9.6
Installed Rmath ──────────────────────── v0.6.1
Installed IteratorInterfaceExtensions ── v1.0.0
Installed DataFrames ─────────────────── v0.21.7
Installed CSV ────────────────────────── v0.6.2
Updating `~/.julia/environments/v1.6/Project.toml`
[c9a035f4] + JWAS v0.9.0
Updating `~/.julia/environments/v1.6/Manifest.toml`
[336ed68f] + CSV v0.6.2
[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
[31c24e10] + Distributions v0.23.12
[48062228] + FilePathsBase v0.8.0
[1a297f60] + FillArrays v0.9.6
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.1
[c9a035f4] + JWAS v0.9.0
[e1d29d7a] + Missings v0.4.4
[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
[92933f4c] + ProgressMeter v1.4.0
[1fd47b50] + QuadGK v2.4.1
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.1
[f50d1b31] + Rmath_jll v0.2.2+1
[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
[ea10d353] + WeakRefStrings v0.6.2
[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 JWAS
Status `/tmp/jl_Q3sQdV/Project.toml`
[336ed68f] CSV v0.6.2
[a93c6f00] DataFrames v0.21.7
[31c24e10] Distributions v0.23.12
[c9a035f4] JWAS v0.9.0
[92933f4c] ProgressMeter v1.4.0
[2913bbd2] StatsBase v0.33.1
[8bb1440f] DelimitedFiles
[b77e0a4c] InteractiveUtils
[37e2e46d] LinearAlgebra
[de0858da] Printf
[9a3f8284] Random
[2f01184e] SparseArrays
[8dfed614] Test
Status `/tmp/jl_Q3sQdV/Manifest.toml`
[336ed68f] CSV v0.6.2
[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
[31c24e10] Distributions v0.23.12
[48062228] FilePathsBase v0.8.0
[1a297f60] FillArrays v0.9.6
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.1
[c9a035f4] JWAS v0.9.0
[e1d29d7a] Missings v0.4.4
[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
[92933f4c] ProgressMeter v1.4.0
[1fd47b50] QuadGK v2.4.1
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+1
[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
[ea10d353] WeakRefStrings v0.6.2
[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...
The delimiter in pedigree.txt is ','.
calculating inbreeding... 8%%|██▏ | ETA: 0:00:03[Kcalculating inbreeding... 100%%|█████████████████████████| Time: 0:00:01[K
Pedigree informatin:
#individuals: 12
#sires: 4
#dams: 5
#founders: 3
Test single-trait GBLUP analysis using complete genomic data
The delimiter in genotypes.txt is ','.
The header (marker IDs) is provided in genotypes.txt.
#markers: 5; #individuals: 7
Checking phenotypes...
Individual IDs (strings) are provided in the first column of the phenotypic data.
Phenotypes for all traits included in the model for individual a7 in the row 5 are missing. This record is deleted.
The number of observations with both genotypes and phenotypes used in the analysis is 4.
The number of observations with both phenotype and pedigree information used in the analysis is 4.
Missing values are found in independent variables: dam.
A Linear Mixed Model was build using model equations:
y1 = intercept + x1*x3 + x2 + x3 + ID + dam + geno
Model Information:
signal (11): Segmentation fault
in expression starting at /home/pkgeval/.julia/packages/JWAS/ddCXV/test/test_BayesianAlphabet.jl:17
uv_write2 at /workspace/srcdir/libuv/src/unix/stream.c:1402
uv_write at /workspace/srcdir/libuv/src/unix/stream.c:1497
jl_uv_write at /workspace/srcdir/src/jl_uv.c:471
uv_write_async at ./stream.jl:1024
uv_write at ./stream.jl:981
unsafe_write at ./stream.jl:1064
unsafe_write at ./io.jl:646 [inlined]
write at ./io.jl:669 [inlined]
format at /workspace/srcdir/usr/share/julia/stdlib/v1.6/Printf/src/Printf.jl:729
#describe#73 at /home/pkgeval/.julia/packages/JWAS/ddCXV/src/1.JWAS/src/JWAS.jl:616
describe at /home/pkgeval/.julia/packages/JWAS/ddCXV/src/1.JWAS/src/JWAS.jl:610 [inlined]
#runMCMC#60 at /home/pkgeval/.julia/packages/JWAS/ddCXV/src/1.JWAS/src/JWAS.jl:268
runMCMC##kw at /home/pkgeval/.julia/packages/JWAS/ddCXV/src/1.JWAS/src/JWAS.jl:155
unknown function (ip: 0x7fe2c1276693)
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
top-level scope at /home/pkgeval/.julia/packages/JWAS/ddCXV/test/test_BayesianAlphabet.jl:52
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:831
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:785
jl_toplevel_eval_in at /workspace/srcdir/src/toplevel.c:880
eval at ./boot.jl:360 [inlined]
include_string at ./loading.jl:1026
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
_include at ./loading.jl:1080
include at ./client.jl:444
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
jl_apply at /workspace/srcdir/src/julia.h:1687 [inlined]
do_call at /workspace/srcdir/src/interpreter.c:115
eval_value at /workspace/srcdir/src/interpreter.c:204
eval_stmt_value at /workspace/srcdir/src/interpreter.c:155 [inlined]
eval_body at /workspace/srcdir/src/interpreter.c:561
jl_interpret_toplevel_thunk at /workspace/srcdir/src/interpreter.c:669
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:837
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:785
jl_toplevel_eval_in at /workspace/srcdir/src/toplevel.c:880
eval at ./boot.jl:360 [inlined]
include_string at ./loading.jl:1026
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
_include at ./loading.jl:1080
include at ./client.jl:444
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
jl_apply at /workspace/srcdir/src/julia.h:1687 [inlined]
do_call at /workspace/srcdir/src/interpreter.c:115
eval_value at /workspace/srcdir/src/interpreter.c:204
eval_stmt_value at /workspace/srcdir/src/interpreter.c:155 [inlined]
eval_body at /workspace/srcdir/src/interpreter.c:561
jl_interpret_toplevel_thunk at /workspace/srcdir/src/interpreter.c:669
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:837
jl_toplevel_eval_flex at /workspace/srcdir/src/toplevel.c:785
jl_toplevel_eval_in at /workspace/srcdir/src/toplevel.c:880
eval at ./boot.jl:360
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
exec_options at ./client.jl:261
_start at ./client.jl:485
jfptr__start_36143.clone_1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /workspace/srcdir/src/gf.c:2192 [inlined]
jl_apply_generic at /workspace/srcdir/src/gf.c:2374
jl_apply at /workspace/srcdir/src/julia.h:1687 [inlined]
true_main at /workspace/srcdir/src/jlapi.c:553
repl_entrypoint at /workspace/srcdir/src/jlapi.c:672
main at /workspace/srcdir/cli/loader_exe.c:46
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x400bae)
Allocations: 118040495 (Pool: 117995451; Big: 45044); GC: 134
ERROR: Package JWAS errored during testing (received signal: 11)
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