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1.5.0-DEV-13d1bd4689.log
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Julia Version 1.5.0-DEV.0
Commit 13d1bd4689 (2019-12-31 18:18 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-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
Resolving package versions...
Installed AxisAlgorithms ────────────── v1.0.0
Installed Reexport ──────────────────── v0.2.0
Installed FFTW_jll ──────────────────── v3.3.9+3
Installed DiffResults ───────────────── v1.0.2
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed DataStructures ────────────── v0.17.6
Installed IterTools ─────────────────── v1.3.0
Installed StanBase ──────────────────── v1.1.3
Installed RecipesBase ───────────────── v0.7.0
Installed Ratios ────────────────────── v0.3.1
Installed DataAPI ───────────────────── v1.1.0
Installed StanSamples ───────────────── v0.1.0
Installed WeakRefStrings ────────────── v0.6.2
Installed Rmath ─────────────────────── v0.6.0
Installed Compat ────────────────────── v2.2.0
Installed DocStringExtensions ───────── v0.8.1
Installed Parsers ───────────────────── v0.3.10
Installed OrderedCollections ────────── v1.1.0
Installed NaNMath ───────────────────── v0.3.3
Installed Arpack ────────────────────── v0.4.0
Installed InvertedIndices ───────────── v1.0.0
Installed StatsFuns ─────────────────── v0.9.3
Installed CommonSubexpressions ──────── v0.2.0
Installed Requires ──────────────────── v1.0.0
Installed Tables ────────────────────── v0.2.11
Installed TableTraits ───────────────── v1.0.0
Installed StanRun ───────────────────── v0.2.1
Installed CSV ───────────────────────── v0.5.21
Installed DiffRules ─────────────────── v1.0.0
Installed AbstractFFTs ──────────────── v0.5.0
Installed ForwardDiff ───────────────── v0.10.8
Installed Interpolations ────────────── v0.12.5
Installed Optim ─────────────────────── v0.19.7
Installed Showoff ───────────────────── v0.3.1
Installed Arpack_jll ────────────────── v3.5.0+2
Installed JSON ──────────────────────── v0.21.0
Installed DataFrames ────────────────── v0.20.0
Installed OpenBLAS_jll ──────────────── v0.3.7+2
Installed BinaryProvider ────────────── v0.5.8
Installed OffsetArrays ──────────────── v0.11.4
Installed MCMCChains ────────────────── v1.0.0
Installed DiffEqDiffTools ───────────── v1.7.0
Installed FFTW ──────────────────────── v1.2.0
Installed RangeArrays ───────────────── v0.3.2
Installed IntelOpenMP_jll ───────────── v2018.0.3+0
Installed ProgressMeter ─────────────── v1.2.0
Installed NamedTupleTools ───────────── v0.12.1
Installed FillArrays ────────────────── v0.8.2
Installed IntervalSets ──────────────── v0.3.2
Installed DataValueInterfaces ───────── v1.0.0
Installed LineSearches ──────────────── v7.0.1
Installed WoodburyMatrices ──────────── v0.4.1
Installed MKL_jll ───────────────────── v2019.0.117+0
Installed Calculus ──────────────────── v0.5.1
Installed AbstractMCMC ──────────────── v0.1.0
Installed SortingAlgorithms ─────────── v0.3.1
Installed PooledArrays ──────────────── v0.5.3
Installed SpecialFunctions ──────────── v0.9.0
Installed PositiveFactorizations ────── v0.2.3
Installed PDMats ────────────────────── v0.9.10
Installed StaticArrays ──────────────── v0.12.1
Installed FilePathsBase ─────────────── v0.7.0
Installed QuadGK ────────────────────── v2.3.1
Installed KernelDensity ─────────────── v0.5.1
Installed ArgCheck ──────────────────── v1.0.1
Installed StanDump ──────────────────── v0.2.0
Installed ArrayInterface ────────────── v2.3.1
Installed Missings ──────────────────── v0.4.3
Installed Parameters ────────────────── v0.12.0
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed ElasticArrays ─────────────── v1.0.0
Installed StatsBase ─────────────────── v0.32.0
Installed NLSolversBase ─────────────── v7.5.0
Installed Distributions ─────────────── v0.21.11
Installed AxisArrays ────────────────── v0.3.3
Installed CategoricalArrays ─────────── v0.7.5
Updating `~/.julia/environments/v1.5/Project.toml`
[d0ee94f6] + StanBase v1.1.3
Updating `~/.julia/environments/v1.5/Manifest.toml`
[621f4979] + AbstractFFTs v0.5.0
[80f14c24] + AbstractMCMC v0.1.0
[dce04be8] + ArgCheck v1.0.1
[7d9fca2a] + Arpack v0.4.0
[68821587] + Arpack_jll v3.5.0+2
[4fba245c] + ArrayInterface v2.3.1
[13072b0f] + AxisAlgorithms v1.0.0
[39de3d68] + AxisArrays v0.3.3
[b99e7846] + BinaryProvider v0.5.8
[336ed68f] + CSV v0.5.21
[49dc2e85] + Calculus v0.5.1
[324d7699] + CategoricalArrays v0.7.5
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.20.0
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[01453d9d] + DiffEqDiffTools v1.7.0
[163ba53b] + DiffResults v1.0.2
[b552c78f] + DiffRules v1.0.0
[31c24e10] + Distributions v0.21.11
[ffbed154] + DocStringExtensions v0.8.1
[fdbdab4c] + ElasticArrays v1.0.0
[7a1cc6ca] + FFTW v1.2.0
[f5851436] + FFTW_jll v3.3.9+3
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[f6369f11] + ForwardDiff v0.10.8
[1d5cc7b8] + IntelOpenMP_jll v2018.0.3+0
[a98d9a8b] + Interpolations v0.12.5
[8197267c] + IntervalSets v0.3.2
[41ab1584] + InvertedIndices v1.0.0
[c8e1da08] + IterTools v1.3.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[5ab0869b] + KernelDensity v0.5.1
[d3d80556] + LineSearches v7.0.1
[c7f686f2] + MCMCChains v1.0.0
[856f044c] + MKL_jll v2019.0.117+0
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.5.0
[77ba4419] + NaNMath v0.3.3
[d9ec5142] + NamedTupleTools v0.12.1
[6fe1bfb0] + OffsetArrays v0.11.4
[4536629a] + OpenBLAS_jll v0.3.7+2
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.19.7
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[2dfb63ee] + PooledArrays v0.5.3
[85a6dd25] + PositiveFactorizations v0.2.3
[92933f4c] + ProgressMeter v1.2.0
[1fd47b50] + QuadGK v2.3.1
[b3c3ace0] + RangeArrays v0.3.2
[c84ed2f1] + Ratios v0.3.1
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v1.0.0
[79098fc4] + Rmath v0.6.0
[992d4aef] + Showoff v0.3.1
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[d0ee94f6] + StanBase v1.1.3
[9713c8f3] + StanDump v0.2.0
[d49c3b98] + StanRun v0.2.1
[52d0d7a9] + StanSamples v0.1.0
[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
[efce3f68] + WoodburyMatrices v0.4.1
[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_c404XN/Project.toml`
[no changes]
Updating `/tmp/jl_c404XN/Manifest.toml`
[no changes]
Building FFTW ─→ `~/.julia/packages/FFTW/qqcBj/deps/build.log`
Updating `/tmp/jl_19rUVU/Project.toml`
[no changes]
Updating `/tmp/jl_19rUVU/Manifest.toml`
[no changes]
Testing StanBase
Updating `/tmp/jl_mMdES8/Project.toml`
[no changes]
Updating `/tmp/jl_mMdES8/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_mMdES8/Project.toml`
[336ed68f] CSV v0.5.21
[a93c6f00] DataFrames v0.20.0
[ffbed154] DocStringExtensions v0.8.1
[c7f686f2] MCMCChains v1.0.0
[d9ec5142] NamedTupleTools v0.12.1
[d96e819e] Parameters v0.12.0
[189a3867] Reexport v0.2.0
[d0ee94f6] StanBase v1.1.3
[9713c8f3] StanDump v0.2.0
[d49c3b98] StanRun v0.2.1
[52d0d7a9] StanSamples v0.1.0
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[9a3f8284] Random
[8dfed614] Test
[4ec0a83e] Unicode
┌ Warning: Environment variable CMDSTAN_HOME not set. Use set_cmdstan_home!.
└ @ StanBase ~/.julia/packages/StanBase/iNJeT/src/StanBase.jl:58
/tmp/jl_4K12Pb/help.stan updated.
Basic HelpModel: Error During Test at /home/pkgeval/.julia/packages/StanBase/iNJeT/test/runtests.jl:20
Got exception outside of a @test
The environment variable JULIA_CMDSTAN_HOME needs to be set.
Stacktrace:
[1] (::StanRun.var"#1#2")() at /home/pkgeval/.julia/packages/StanRun/E3YcJ/src/StanRun.jl:25
[2] (::Base.var"#463#464"{StanRun.var"#1#2"})(::String) at ./env.jl:81
[3] access_env at ./env.jl:43 [inlined]
[4] get at ./env.jl:81 [inlined]
[5] get_cmdstan_home at /home/pkgeval/.julia/packages/StanRun/E3YcJ/src/StanRun.jl:24 [inlined]
[6] StanModel at /home/pkgeval/.julia/packages/StanRun/E3YcJ/src/StanRun.jl:82 [inlined]
[7] HelpModel(::String, ::String, ::Array{Int64,1}; seed::StanBase.RandomSeed, init::StanBase.Init, output::StanBase.Output, tmpdir::String, method::StanBase.Help, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /home/pkgeval/.julia/packages/StanBase/iNJeT/src/stanmodel/HelpModel.jl:23
[8] HelpModel at /home/pkgeval/.julia/packages/StanBase/iNJeT/src/stanmodel/HelpModel.jl:20 [inlined] (repeats 2 times)
[9] macro expansion at /home/pkgeval/.julia/packages/StanBase/iNJeT/test/runtests.jl:22 [inlined]
[10] macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1116 [inlined]
[11] top-level scope at /home/pkgeval/.julia/packages/StanBase/iNJeT/test/runtests.jl:22
[12] include(::String) at ./client.jl:439
[13] top-level scope at none:6
[14] eval(::Module, ::Any) at ./boot.jl:331
[15] exec_options(::Base.JLOptions) at ./client.jl:264
[16] _start() at ./client.jl:484
signal (15): Terminated
in expression starting at none:12
epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
uv__io_poll at /workspace/srcdir/libuv/src/unix/linux-core.c:270
uv_run at /workspace/srcdir/libuv/src/unix/core.c:359
jl_task_get_next at /buildworker/worker/package_linux64/build/src/partr.c:449
poptaskref at ./task.jl:702
wait at ./task.jl:709
wait at ./condition.jl:106
wait at ./process.jl:622
success at ./process.jl:483 [inlined]
#run#561 at ./process.jl:440
run at ./process.jl:438 [inlined]
#93 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1460
withenv at ./env.jl:161
#85 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1369
with_temp_env at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1283
#84 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1354
#mktempdir#20 at ./file.jl:673
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2158 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2322
mktempdir at ./file.jl:671
mktempdir at ./file.jl:671 [inlined]
sandbox at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1321
#test#92 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1454
test##kw at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1418 [inlined]
#test#67 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:313
test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:300
#test#66 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
#test#65 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
#test#64 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2158 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2322
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1692 [inlined]
do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:643
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2144 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2322
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1692 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:369
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:458
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:409 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:817
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:911
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:814
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:843
eval at ./boot.jl:331
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2144 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2322
exec_options at ./client.jl:264
_start at ./client.jl:484
jfptr__start_2076.clone_1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2144 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2322
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1692 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:96
main at /buildworker/worker/package_linux64/build/ui/repl.c:217
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /opt/julia/bin/julia (unknown line)
unknown function (ip: (nil))
Allocations: 22206853 (Pool: 22200067; Big: 6786); GC: 27