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1.5.0-DEV-7206b56e94.log
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Julia Version 1.5.0-DEV.485
Commit 7206b56e94 (2020-03-18 17:25 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-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed SortingAlgorithms ─────────── v0.3.1
Installed Widgets ───────────────────── v0.6.2
Installed FunctionalCollections ─────── v0.5.0
Installed LaTeXStrings ──────────────── v1.1.0
Installed Conda ─────────────────────── v1.4.1
Installed TextWrap ──────────────────── v1.0.1
Installed VariantVisualization ──────── v0.4.0
Installed DataFrames ────────────────── v0.20.2
Installed BinDeps ───────────────────── v1.0.0
Installed WebIO ─────────────────────── v0.8.11
Installed DataValueInterfaces ───────── v1.0.0
Installed VersionParsing ────────────── v1.2.0
Installed Observables ───────────────── v0.3.1
Installed ORCA ──────────────────────── v0.3.1
Installed FixedPointNumbers ─────────── v0.7.1
Installed CodecZlib ─────────────────── v0.7.0
Installed WebSockets ────────────────── v1.5.2
Installed CategoricalArrays ─────────── v0.7.7
Installed DocStringExtensions ───────── v0.8.1
Installed Zlib_jll ──────────────────── v1.2.11+8
Installed Combinatorics ─────────────── v0.7.0
Installed PlotlyJS ──────────────────── v0.13.1
Installed JSON ──────────────────────── v0.21.0
Installed MbedTLS_jll ───────────────── v2.16.0+1
Installed Pidfile ───────────────────── v1.1.0
Installed Reexport ──────────────────── v0.2.0
Installed Hiccup ────────────────────── v0.2.2
Installed ColorTypes ────────────────── v0.9.1
Installed DataStructures ────────────── v0.17.10
Installed ArgParse ──────────────────── v1.1.0
Installed RecipesBase ───────────────── v0.8.0
Installed PooledArrays ──────────────── v0.5.3
Installed AssetRegistry ─────────────── v0.1.0
Installed JSExpr ────────────────────── v0.5.0
Installed InvertedIndices ───────────── v1.0.0
Installed Parsers ───────────────────── v0.3.12
Installed Polynomials ───────────────── v0.6.1
Installed DataAPI ───────────────────── v1.1.0
Installed YAML ──────────────────────── v0.4.0
Installed IniFile ───────────────────── v0.5.0
Installed Missings ──────────────────── v0.4.3
Installed Mux ───────────────────────── v0.7.1
Installed HTTP ──────────────────────── v0.8.12
Installed Requires ──────────────────── v1.0.1
Installed Lazy ──────────────────────── v0.14.0
Installed BufferedStreams ───────────── v1.0.0
Installed Colors ────────────────────── v0.11.2
Installed GeneticVariation ──────────── v0.4.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed IndexableBitVectors ───────── v1.0.0
Installed Automa ────────────────────── v0.8.0
Installed Twiddle ───────────────────── v1.1.1
Installed Tables ────────────────────── v1.0.3
Installed Mustache ──────────────────── v0.5.13
Installed BioSymbols ────────────────── v3.1.0
Installed MacroTools ────────────────── v0.5.4
Installed URIParser ─────────────────── v0.4.0
Installed BGZFStreams ───────────────── v0.3.0
Installed PlotlyBase ────────────────── v0.3.0
Installed Blink ─────────────────────── v0.12.2
Installed MbedTLS ───────────────────── v1.0.1
Installed OrderedCollections ────────── v1.1.0
Installed Compat ────────────────────── v2.2.0
Installed TableTraits ───────────────── v1.0.0
Installed BioCore ───────────────────── v2.0.5
Installed TranscodingStreams ────────── v0.9.5
Installed IntervalTrees ─────────────── v1.0.0
Installed BioSequences ──────────────── v1.1.0
#=#=# ######################################################################## 100.0%
#=#=# ##################################### 51.8%######################################################################## 100.0%
Updating `~/.julia/environments/v1.5/Project.toml`
7f8bf45c + VariantVisualization v0.4.0
Updating `~/.julia/environments/v1.5/Manifest.toml`
c7e460c6 + ArgParse v1.1.0
bf4720bc + AssetRegistry v0.1.0
67c07d97 + Automa v0.8.0
28d598bf + BGZFStreams v0.3.0
9e28174c + BinDeps v1.0.0
37cfa864 + BioCore v2.0.5
7e6ae17a + BioSequences v1.1.0
3c28c6f8 + BioSymbols v3.1.0
ad839575 + Blink v0.12.2
e1450e63 + BufferedStreams v1.0.0
324d7699 + CategoricalArrays v0.7.7
944b1d66 + CodecZlib v0.7.0
3da002f7 + ColorTypes v0.9.1
5ae59095 + Colors v0.11.2
861a8166 + Combinatorics v0.7.0
34da2185 + Compat v2.2.0
8f4d0f93 + Conda v1.4.1
9a962f9c + DataAPI v1.1.0
a93c6f00 + DataFrames v0.20.2
864edb3b + DataStructures v0.17.10
e2d170a0 + DataValueInterfaces v1.0.0
ffbed154 + DocStringExtensions v0.8.1
53c48c17 + FixedPointNumbers v0.7.1
de31a74c + FunctionalCollections v0.5.0
9bc6ac9d + GeneticVariation v0.4.0
cd3eb016 + HTTP v0.8.12
9fb69e20 + Hiccup v0.2.2
1cb3b9ac + IndexableBitVectors v1.0.0
83e8ac13 + IniFile v0.5.0
524e6230 + IntervalTrees v1.0.0
41ab1584 + InvertedIndices v1.0.0
82899510 + IteratorInterfaceExtensions v1.0.0
97c1335a + JSExpr v0.5.0
682c06a0 + JSON v0.21.0
b964fa9f + LaTeXStrings v1.1.0
50d2b5c4 + Lazy v0.14.0
1914dd2f + MacroTools v0.5.4
739be429 + MbedTLS v1.0.1
c8ffd9c3 + MbedTLS_jll v2.16.0+1
e1d29d7a + Missings v0.4.3
ffc61752 + Mustache v0.5.13
a975b10e + Mux v0.7.1
47be7bcc + ORCA v0.3.1
510215fc + Observables v0.3.1
bac558e1 + OrderedCollections v1.1.0
69de0a69 + Parsers v0.3.12
fa939f87 + Pidfile v1.1.0
a03496cd + PlotlyBase v0.3.0
f0f68f2c + PlotlyJS v0.13.1
f27b6e38 + Polynomials v0.6.1
2dfb63ee + PooledArrays v0.5.3
3cdcf5f2 + RecipesBase v0.8.0
189a3867 + Reexport v0.2.0
ae029012 + Requires v1.0.1
a2af1166 + SortingAlgorithms v0.3.1
3783bdb8 + TableTraits v1.0.0
bd369af6 + Tables v1.0.3
b718987f + TextWrap v1.0.1
3bb67fe8 + TranscodingStreams v0.9.5
7200193e + Twiddle v1.1.1
30578b45 + URIParser v0.4.0
7f8bf45c + VariantVisualization v0.4.0
81def892 + VersionParsing v1.2.0
0f1e0344 + WebIO v0.8.11
104b5d7c + WebSockets v1.5.2
cc8bc4a8 + Widgets v0.6.2
ddb6d928 + YAML v0.4.0
83775a58 + Zlib_jll v1.2.11+8
2a0f44e3 + Base64
ade2ca70 + Dates
8bb1440f + DelimitedFiles
8ba89e20 + Distributed
7b1f6079 + FileWatching
9fa8497b + Future
b77e0a4c + InteractiveUtils
76f85450 + LibGit2
8f399da3 + Libdl
37e2e46d + LinearAlgebra
56ddb016 + Logging
d6f4376e + Markdown
a63ad114 + Mmap
44cfe95a + Pkg
de0858da + Printf
9abbd945 + Profile
3fa0cd96 + REPL
9a3f8284 + Random
ea8e919c + SHA
9e88b42a + Serialization
1a1011a3 + SharedArrays
6462fe0b + Sockets
2f01184e + SparseArrays
10745b16 + Statistics
8dfed614 + Test
cf7118a7 + UUIDs
4ec0a83e + Unicode
Building WebIO ───────────────→ `~/.julia/packages/WebIO/2mZPb/deps/build.log`
Building Blink ───────────────→ `~/.julia/packages/Blink/HhoiS/deps/build.log`
Building PlotlyJS ────────────→ `~/.julia/packages/PlotlyJS/AhkM5/deps/build.log`
Building Conda ───────────────→ `~/.julia/packages/Conda/3rPhK/deps/build.log`
Building ORCA ────────────────→ `~/.julia/packages/ORCA/fiEmb/deps/build.log`
Building VariantVisualization → `~/.julia/packages/VariantVisualization/1yoNl/deps/build.log`
┌ Error: Error building `VariantVisualization`:
│ ERROR: LoadError: IOError: symlink: permission denied (EACCES)
│ Stacktrace:
│ [1] uv_error at ./libuv.jl:97 [inlined]
│ [2] symlink(::String, ::String) at ./file.jl:958
│ [3] symlink_user_bin(::String) at /home/pkgeval/.julia/packages/VariantVisualization/1yoNl/deps/build.jl:18
│ [4] top-level scope at /home/pkgeval/.julia/packages/VariantVisualization/1yoNl/deps/build.jl:24
│ [5] include(::String) at ./client.jl:441
│ [6] top-level scope at none:5
│ in expression starting at /home/pkgeval/.julia/packages/VariantVisualization/1yoNl/deps/build.jl:24
└ @ Pkg.Operations /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:912
Testing VariantVisualization
Status `/tmp/jl_97Wyxs/Project.toml`
c7e460c6 ArgParse v1.1.0
a93c6f00 DataFrames v0.20.2
9bc6ac9d GeneticVariation v0.4.0
47be7bcc ORCA v0.3.1
f0f68f2c PlotlyJS v0.13.1
7f8bf45c VariantVisualization v0.4.0
8bb1440f DelimitedFiles
8dfed614 Test
Status `/tmp/jl_97Wyxs/Manifest.toml`
c7e460c6 ArgParse v1.1.0
bf4720bc AssetRegistry v0.1.0
67c07d97 Automa v0.8.0
28d598bf BGZFStreams v0.3.0
9e28174c BinDeps v1.0.0
37cfa864 BioCore v2.0.5
7e6ae17a BioSequences v1.1.0
3c28c6f8 BioSymbols v3.1.0
ad839575 Blink v0.12.2
e1450e63 BufferedStreams v1.0.0
324d7699 CategoricalArrays v0.7.7
944b1d66 CodecZlib v0.7.0
3da002f7 ColorTypes v0.9.1
5ae59095 Colors v0.11.2
861a8166 Combinatorics v0.7.0
34da2185 Compat v2.2.0
8f4d0f93 Conda v1.4.1
9a962f9c DataAPI v1.1.0
a93c6f00 DataFrames v0.20.2
864edb3b DataStructures v0.17.10
e2d170a0 DataValueInterfaces v1.0.0
ffbed154 DocStringExtensions v0.8.1
53c48c17 FixedPointNumbers v0.7.1
de31a74c FunctionalCollections v0.5.0
9bc6ac9d GeneticVariation v0.4.0
cd3eb016 HTTP v0.8.12
9fb69e20 Hiccup v0.2.2
1cb3b9ac IndexableBitVectors v1.0.0
83e8ac13 IniFile v0.5.0
524e6230 IntervalTrees v1.0.0
41ab1584 InvertedIndices v1.0.0
82899510 IteratorInterfaceExtensions v1.0.0
97c1335a JSExpr v0.5.0
682c06a0 JSON v0.21.0
b964fa9f LaTeXStrings v1.1.0
50d2b5c4 Lazy v0.14.0
1914dd2f MacroTools v0.5.4
739be429 MbedTLS v1.0.1
c8ffd9c3 MbedTLS_jll v2.16.0+1
e1d29d7a Missings v0.4.3
ffc61752 Mustache v0.5.13
a975b10e Mux v0.7.1
47be7bcc ORCA v0.3.1
510215fc Observables v0.3.1
bac558e1 OrderedCollections v1.1.0
69de0a69 Parsers v0.3.12
fa939f87 Pidfile v1.1.0
a03496cd PlotlyBase v0.3.0
f0f68f2c PlotlyJS v0.13.1
f27b6e38 Polynomials v0.6.1
2dfb63ee PooledArrays v0.5.3
3cdcf5f2 RecipesBase v0.8.0
189a3867 Reexport v0.2.0
ae029012 Requires v1.0.1
a2af1166 SortingAlgorithms v0.3.1
3783bdb8 TableTraits v1.0.0
bd369af6 Tables v1.0.3
b718987f TextWrap v1.0.1
3bb67fe8 TranscodingStreams v0.9.5
7200193e Twiddle v1.1.1
30578b45 URIParser v0.4.0
7f8bf45c VariantVisualization v0.4.0
81def892 VersionParsing v1.2.0
0f1e0344 WebIO v0.8.11
104b5d7c WebSockets v1.5.2
cc8bc4a8 Widgets v0.6.2
ddb6d928 YAML v0.4.0
83775a58 Zlib_jll v1.2.11+8
2a0f44e3 Base64
ade2ca70 Dates
8bb1440f DelimitedFiles
8ba89e20 Distributed
7b1f6079 FileWatching
9fa8497b Future
b77e0a4c InteractiveUtils
76f85450 LibGit2
8f399da3 Libdl
37e2e46d LinearAlgebra
56ddb016 Logging
d6f4376e Markdown
a63ad114 Mmap
44cfe95a Pkg
de0858da Printf
9abbd945 Profile
3fa0cd96 REPL
9a3f8284 Random
ea8e919c SHA
9e88b42a Serialization
1a1011a3 SharedArrays
6462fe0b Sockets
2f01184e SparseArrays
10745b16 Statistics
8dfed614 Test
cf7118a7 UUIDs
4ec0a83e Unicode
┌ Warning: `@get!(dict, key, default)` at /home/pkgeval/.julia/packages/WebIO/2mZPb/src/scope.jl:160 is deprecated, use `get!(()->default, dict, key)` instead.
│ caller = include(::Function, ::Module, ::String) at Base.jl:380
└ @ Base ./Base.jl:380
┌ Warning: `@get!(dict, key, default)` at /home/pkgeval/.julia/packages/Lazy/mAoZN/src/collections.jl:49 is deprecated, use `get!(()->default, dict, key)` instead.
│ caller = include(::Function, ::Module, ::String) at Base.jl:380
└ @ Base ./Base.jl:380
ERROR: LoadError: InitError: IOError: could not spawn `'/usr/bin/xvfb-run /home/pkgeval/.julia/conda/3/envs/_ORCA_jl_/bin/orca' server --port=7982 --graph-only`: no such file or directory (ENOENT)
Stacktrace:
[1] _spawn_primitive(::String, ::Cmd, ::Array{Any,1}) at ./process.jl:99
[2] #564 at ./process.jl:112 [inlined]
[3] setup_stdios(::Base.var"#564#565"{Cmd}, ::Array{Any,1}) at ./process.jl:196
[4] _spawn at ./process.jl:111 [inlined]
[5] open(::Cmd, ::Base.DevNull; write::Bool, read::Bool) at ./process.jl:370
[6] open at ./process.jl:361 [inlined] (repeats 2 times)
[7] restart_server() at /home/pkgeval/.julia/packages/ORCA/fiEmb/src/ORCA.jl:84
[8] __init__() at /home/pkgeval/.julia/packages/ORCA/fiEmb/src/ORCA.jl:94
[9] _include_from_serialized(::String, ::Array{Any,1}) at ./loading.jl:697
[10] _require_from_serialized(::String) at ./loading.jl:748
[11] _require(::Base.PkgId) at ./loading.jl:1039
[12] require(::Base.PkgId) at ./loading.jl:927
[13] require(::Module, ::Symbol) at ./loading.jl:922
[14] include(::Function, ::Module, ::String) at ./Base.jl:380
[15] include(::Module, ::String) at ./Base.jl:368
[16] top-level scope at none:2
[17] eval at ./boot.jl:331 [inlined]
[18] eval(::Expr) at ./client.jl:451
[19] top-level scope at ./none:3
during initialization of module ORCA
in expression starting at /home/pkgeval/.julia/packages/VariantVisualization/1yoNl/src/VariantVisualization.jl:5
ERROR: LoadError: Failed to precompile VariantVisualization [7f8bf45c-0ad5-53b5-97e6-33c1305e0aa4] to /home/pkgeval/.julia/compiled/v1.5/VariantVisualization/v8cR2_ZrefO.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1288
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::String) at ./client.jl:441
[7] top-level scope at none:6
in expression starting at /home/pkgeval/.julia/packages/VariantVisualization/1yoNl/test/runtests.jl:3
ERROR: Package VariantVisualization errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:53
[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/v1.5/Pkg/src/Operations.jl:1523
[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/v1.5/Pkg/src/API.jl:316
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:303
[5] #test#68 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[6] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[7] #test#67 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[8] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[10] test(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[11] top-level scope at none:13