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1.5.0-DEV-f014071421.log
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Julia Version 1.5.0-DEV.232
Commit f014071421 (2020-02-03 21:36 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 YAML ──────────────── v0.3.2
Installed RecipesBase ───────── v0.7.0
Installed BGZFStreams ───────── v0.3.0
Installed Libz ──────────────── v1.0.1
Installed CodecZlib ─────────── v0.6.0
Installed CAOS ──────────────── v0.1.1
Installed BufferedStreams ───── v1.0.0
Installed EzXML ─────────────── v0.9.5
Installed Tokenize ──────────── v0.5.7
Installed BioCore ───────────── v2.0.5
Installed ColorTypes ────────── v0.9.1
Installed TranscodingStreams ── v0.9.5
Installed IntervalTrees ─────── v1.0.0
Installed JSON ──────────────── v0.21.0
Installed BioAlignments ─────── v1.0.1
Installed BioSequences ──────── v1.1.0
Installed Codecs ────────────── v0.5.0
Installed Combinatorics ─────── v0.7.0
Installed GZip ──────────────── v0.5.1
Installed IndexableBitVectors ─ v1.0.0
Installed BioSymbols ────────── v3.1.0
Installed FastaIO ───────────── v0.5.0
Installed DataStructures ────── v0.17.9
Installed Automa ────────────── v0.8.0
Installed BinaryProvider ────── v0.5.8
Installed Parsers ───────────── v0.3.11
Installed Twiddle ───────────── v1.1.1
Installed BioTools ──────────── v1.0.0
Installed URIParser ─────────── v0.4.0
Installed Compat ────────────── v2.2.0
Installed FixedPointNumbers ─── v0.7.1
Installed OrderedCollections ── v1.1.0
Installed Polynomials ───────── v0.6.0
Installed GenomicFeatures ───── v1.0.4
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 v1.0.1
[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 v0.9.1
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.2.0
[864edb3b] + DataStructures v0.17.9
[8f5d6c58] + EzXML v0.9.5
[a0c94c4b] + FastaIO v0.5.0
[53c48c17] + FixedPointNumbers v0.7.1
[92fee26a] + GZip v0.5.1
[899a7d2d] + GenomicFeatures v1.0.4
[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 v0.3.11
[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`
Building EzXML ────→ `~/.julia/packages/EzXML/QtGgF/deps/build.log`
Testing CAOS
Status `/tmp/jl_COpJQI/Manifest.toml`
[67c07d97] Automa v0.8.0
[28d598bf] BGZFStreams v0.3.0
[b99e7846] BinaryProvider v0.5.8
[00701ae9] BioAlignments v1.0.1
[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 v0.9.1
[861a8166] Combinatorics v0.7.0
[34da2185] Compat v2.2.0
[864edb3b] DataStructures v0.17.9
[8f5d6c58] EzXML v0.9.5
[a0c94c4b] FastaIO v0.5.0
[53c48c17] FixedPointNumbers v0.7.1
[92fee26a] GZip v0.5.1
[899a7d2d] GenomicFeatures v1.0.4
[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 v0.3.11
[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
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] #555 at ./process.jl:112 [inlined]
[3] setup_stdios(::Base.var"#555#556"{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(::String, ::String) at /home/pkgeval/.julia/packages/CAOS/NDV79/src/user_functions.jl:14
[9] top-level scope at /home/pkgeval/.julia/packages/CAOS/NDV79/test/classification.jl:3
[10] top-level scope at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1114
[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
ERROR: Package CAOS 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:1503
[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