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1.5.0-DEV-13d1bd4689.log
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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 RecipesBase ───────── v0.7.0
Installed Compat ────────────── v2.2.0
Installed Tokenize ──────────── v0.5.7
Installed IndexableBitVectors ─ v1.0.0
Installed DataStructures ────── v0.17.6
Installed BioSymbols ────────── v3.1.0
Installed CAOS ──────────────── v0.1.1
Installed BioAlignments ─────── v1.0.0
Installed OrderedCollections ── v1.1.0
Installed FastaIO ───────────── v0.5.0
Installed Parsers ───────────── v0.3.10
Installed BGZFStreams ───────── v0.3.0
Installed CodecZlib ─────────── v0.6.0
Installed FixedPointNumbers ─── v0.5.3
Installed Twiddle ───────────── v1.1.1
Installed Polynomials ───────── v0.6.0
Installed BinaryProvider ────── v0.5.8
Installed URIParser ─────────── v0.4.0
Installed YAML ──────────────── v0.3.2
Installed JSON ──────────────── v0.21.0
Installed EzXML ─────────────── v0.9.5
Installed TranscodingStreams ── v0.9.5
Installed ColorTypes ────────── v0.9.0
Installed Automa ────────────── v0.8.0
Installed IntervalTrees ─────── v1.0.0
Installed GZip ──────────────── v0.5.1
Installed Combinatorics ─────── v0.7.0
Installed BufferedStreams ───── v1.0.0
Installed Codecs ────────────── v0.5.0
Installed BioTools ──────────── v1.0.0
Installed GenomicFeatures ───── v1.0.0
Installed Libz ──────────────── v1.0.1
Installed BioSequences ──────── v1.1.0
Installed BioCore ───────────── v2.0.5
Updating `~/.julia/environments/v1.5/Project.toml`
[84b91ece] + CAOS v0.1.1
Updating `~/.julia/environments/v1.5/Manifest.toml`
[67c07d97] + Automa v0.8.0
[28d598bf] + BGZFStreams v0.3.0
[b99e7846] + BinaryProvider v0.5.8
[00701ae9] + BioAlignments v1.0.0
[37cfa864] + BioCore v2.0.5
[7e6ae17a] + BioSequences v1.1.0
[3c28c6f8] + BioSymbols v3.1.0
[fa51a905] + BioTools v1.0.0
[e1450e63] + BufferedStreams v1.0.0
[84b91ece] + CAOS v0.1.1
[944b1d66] + CodecZlib v0.6.0
[19ecbf4d] + Codecs v0.5.0
[3da002f7] + ColorTypes v0.9.0
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.2.0
[864edb3b] + DataStructures v0.17.6
[8f5d6c58] + EzXML v0.9.5
[a0c94c4b] + FastaIO v0.5.0
[53c48c17] + FixedPointNumbers v0.5.3
[92fee26a] + GZip v0.5.1
[899a7d2d] + GenomicFeatures v1.0.0
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[682c06a0] + JSON v0.21.0
[2ec943e9] + Libz v1.0.1
[bac558e1] + OrderedCollections v1.1.0
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[3cdcf5f2] + RecipesBase v0.7.0
[0796e94c] + Tokenize v0.5.7
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.1
[30578b45] + URIParser v0.4.0
[ddb6d928] + YAML v0.3.2
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[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 CodecZlib → `~/.julia/packages/CodecZlib/5t9zO/deps/build.log`
Updating `/tmp/jl_ms2hcd/Project.toml`
[no changes]
Updating `/tmp/jl_ms2hcd/Manifest.toml`
[no changes]
Building EzXML ────→ `~/.julia/packages/EzXML/QtGgF/deps/build.log`
Updating `/tmp/jl_9KMhjk/Project.toml`
[no changes]
Updating `/tmp/jl_9KMhjk/Manifest.toml`
[no changes]
Testing CAOS
Updating `/tmp/jl_6zmsER/Project.toml`
[no changes]
Updating `/tmp/jl_6zmsER/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_6zmsER/Project.toml`
[00701ae9] BioAlignments v1.0.0
[7e6ae17a] BioSequences v1.1.0
[fa51a905] BioTools v1.0.0
[84b91ece] CAOS v0.1.1
[a0c94c4b] FastaIO v0.5.0
[682c06a0] JSON v0.21.0
[0796e94c] Tokenize v0.5.7
[8dfed614] Test
Running tests:
-----------------------------------------
Testing: Tree functions
Test Summary: | Pass Total
tree_functions | 80 80
-----------------------------------------
Testing: Classification
classification: Error During Test at /home/pkgeval/.julia/packages/CAOS/NDV79/test/classification.jl:1
Got exception outside of a @test
IOError: could not spawn `makeblastdb -in data/output/char_labels.fasta -dbtype nucl`: no such file or directory (ENOENT)
Stacktrace:
[1] _spawn_primitive(::String, ::Cmd, ::Array{Any,1}) at ./process.jl:99
[2] #550 at ./process.jl:112 [inlined]
[3] setup_stdios(::Base.var"#550#551"{Cmd}, ::Array{Any,1}) at ./process.jl:196
[4] _spawn at ./process.jl:111 [inlined]
[5] run(::Cmd; wait::Bool) at ./process.jl:439
[6] run at ./process.jl:438 [inlined]
[7] generate_caos_rules(::String, ::String; protein::Bool) at /home/pkgeval/.julia/packages/CAOS/NDV79/src/user_functions.jl:48
[8] generate_caos_rules at /home/pkgeval/.julia/packages/CAOS/NDV79/src/user_functions.jl:14 [inlined]
[9] macro expansion at /home/pkgeval/.julia/packages/CAOS/NDV79/test/classification.jl:3 [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/CAOS/NDV79/test/classification.jl:3
[12] include(::Module, ::String) at ./Base.jl:377
[13] include(::String) at /home/pkgeval/.julia/packages/CAOS/NDV79/test/runtests.jl:1
[14] top-level scope at /home/pkgeval/.julia/packages/CAOS/NDV79/test/runtests.jl:21
[15] include(::String) at ./client.jl:439
[16] top-level scope at none:6
[17] eval(::Module, ::Any) at ./boot.jl:331
[18] exec_options(::Base.JLOptions) at ./client.jl:264
[19] _start() at ./client.jl:484
Test Summary: | Error Total
classification | 1 1
ERROR: LoadError: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/CAOS/NDV79/test/classification.jl:1
in expression starting at /home/pkgeval/.julia/packages/CAOS/NDV79/test/runtests.jl:18
err = ProcessFailedException(Base.Process[Process(`/opt/julia/bin/julia -Cnative -J/opt/julia/lib/julia/sys.so -g1 --code-coverage=none --color=no --compiled-modules=yes --check-bounds=yes --inline=yes --startup-file=no --track-allocation=none --eval 'append!(empty!(Base.DEPOT_PATH), ["/home/pkgeval/.julia", "/opt/julia/local/share/julia", "/opt/julia/share/julia", "/usr/local/share/julia"])
append!(empty!(Base.DL_LOAD_PATH), String[])
cd("/home/pkgeval/.julia/packages/CAOS/NDV79/test")
append!(empty!(ARGS), String[])
include("/home/pkgeval/.julia/packages/CAOS/NDV79/test/runtests.jl")
'`, ProcessExited(1))])
ERROR: Package CAOS errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:54
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1471
[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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:313
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:300
[5] #test#66 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
[6] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
[7] #test#65 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
[8] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
[10] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
[11] top-level scope at none:12