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1.6.0-DEV-3bfcb743c2.log
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Julia Version 1.6.0-DEV.1185
Commit 3bfcb743c2 (2020-10-11 23:29 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: AMD EPYC 7502 32-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-10.0.1 (ORCJIT, znver2)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
JULIA_MAX_NUM_PRECOMPILE_FILES = 9223372036854775807
Resolving package versions...
Installed URIParser ─────────── v0.4.1
Installed IndexableBitVectors ─ v1.0.0
Installed Parsers ───────────── v1.0.11
Installed Automa ────────────── v0.7.0
Installed CAOS ──────────────── v0.1.2
Installed BioTools ──────────── v1.0.0
Installed JSON ──────────────── v0.21.1
Installed BioSequences ──────── v1.1.0
Installed BioCore ───────────── v2.0.5
Installed Tokenize ──────────── v0.5.8
Installed Twiddle ───────────── v1.1.2
Installed OrderedCollections ── v1.3.1
Installed BGZFStreams ───────── v0.3.0
Installed ColorTypes ────────── v0.9.1
Installed DataStructures ────── v0.17.20
Installed GenomicFeatures ───── v1.0.4
Installed BioAlignments ─────── v1.0.1
Installed FastaIO ───────────── v1.0.0
Installed GZip ──────────────── v0.5.1
Installed TranscodingStreams ── v0.9.5
Installed BioSymbols ────────── v3.1.0
Installed Polynomials ───────── v0.6.1
Installed BinaryProvider ────── v0.5.10
Installed JLLWrappers ───────── v1.1.1
Installed Libz ──────────────── v1.0.1
Installed BufferedStreams ───── v1.0.0
Installed RecipesBase ───────── v0.8.0
Installed IntervalTrees ─────── v1.0.0
Installed Combinatorics ─────── v0.7.0
Installed Zlib_jll ──────────── v1.2.11+17
Installed CodecZlib ─────────── v0.7.0
Installed Compat ────────────── v3.20.0
Installed EzXML ─────────────── v0.9.5
Installed FixedPointNumbers ─── v0.7.1
Installed YAML ──────────────── v0.4.2
Updating `~/.julia/environments/v1.6/Project.toml`
[84b91ece] + CAOS v0.1.2
Updating `~/.julia/environments/v1.6/Manifest.toml`
[67c07d97] + Automa v0.7.0
[28d598bf] + BGZFStreams v0.3.0
[b99e7846] + BinaryProvider v0.5.10
[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 v0.1.2
[944b1d66] + CodecZlib v0.7.0
[3da002f7] + ColorTypes v0.9.1
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v3.20.0
[864edb3b] + DataStructures v0.17.20
[8f5d6c58] + EzXML v0.9.5
[a0c94c4b] + FastaIO v1.0.0
[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
[692b3bcd] + JLLWrappers v1.1.1
[682c06a0] + JSON v0.21.1
[2ec943e9] + Libz v1.0.1
[bac558e1] + OrderedCollections v1.3.1
[69de0a69] + Parsers v1.0.11
[f27b6e38] + Polynomials v0.6.1
[3cdcf5f2] + RecipesBase v0.8.0
[0796e94c] + Tokenize v0.5.8
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.2
[30578b45] + URIParser v0.4.1
[ddb6d928] + YAML v0.4.2
[83775a58] + Zlib_jll v1.2.11+17
[56f22d72] + Artifacts
[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
[fa267f1f] + TOML
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building EzXML → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/469de9cb996a9c03f31905619ff3c33e905711f3/build.log`
Testing CAOS
Status `/tmp/jl_7lkFIY/Project.toml`
[00701ae9] BioAlignments v1.0.1
[7e6ae17a] BioSequences v1.1.0
[fa51a905] BioTools v1.0.0
[84b91ece] CAOS v0.1.2
[a0c94c4b] FastaIO v1.0.0
[682c06a0] JSON v0.21.1
[0796e94c] Tokenize v0.5.8
[8dfed614] Test
Status `/tmp/jl_7lkFIY/Manifest.toml`
[67c07d97] Automa v0.7.0
[28d598bf] BGZFStreams v0.3.0
[b99e7846] BinaryProvider v0.5.10
[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 v0.1.2
[944b1d66] CodecZlib v0.7.0
[3da002f7] ColorTypes v0.9.1
[861a8166] Combinatorics v0.7.0
[34da2185] Compat v3.20.0
[864edb3b] DataStructures v0.17.20
[8f5d6c58] EzXML v0.9.5
[a0c94c4b] FastaIO v1.0.0
[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
[692b3bcd] JLLWrappers v1.1.1
[682c06a0] JSON v0.21.1
[2ec943e9] Libz v1.0.1
[bac558e1] OrderedCollections v1.3.1
[69de0a69] Parsers v1.0.11
[f27b6e38] Polynomials v0.6.1
[3cdcf5f2] RecipesBase v0.8.0
[0796e94c] Tokenize v0.5.8
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.2
[30578b45] URIParser v0.4.1
[ddb6d928] YAML v0.4.2
[83775a58] Zlib_jll v1.2.11+17
[56f22d72] Artifacts
[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
[fa267f1f] TOML
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
Testing Running tests...
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/6lJsa/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(file::String, cmd::Cmd, stdio::Vector{Any})
@ Base ./process.jl:99
[2] #621
@ ./process.jl:112 [inlined]
[3] setup_stdios(f::Base.var"#621#622"{Cmd}, stdios::Vector{Any})
@ Base ./process.jl:196
[4] _spawn
@ ./process.jl:111 [inlined]
[5] run(::Cmd; wait::Bool)
@ Base ./process.jl:439
[6] run
@ ./process.jl:438 [inlined]
[7] generate_caos_rules(tree_file_path::String, output_directory::String; protein::Bool)
@ CAOS ~/.julia/packages/CAOS/6lJsa/src/user_functions.jl:48
[8] generate_caos_rules(tree_file_path::String, output_directory::String)
@ CAOS ~/.julia/packages/CAOS/6lJsa/src/user_functions.jl:14
[9] top-level scope
@ ~/.julia/packages/CAOS/6lJsa/test/classification.jl:3
[10] top-level scope
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144
[11] top-level scope
@ ~/.julia/packages/CAOS/6lJsa/test/classification.jl:3
[12] include(mod::Module, _path::String)
@ Base ./Base.jl:389
[13] include(x::String)
@ Main.TestCAOS ~/.julia/packages/CAOS/6lJsa/test/runtests.jl:1
[14] top-level scope
@ ~/.julia/packages/CAOS/6lJsa/test/runtests.jl:21
[15] include(fname::String)
@ Base.MainInclude ./client.jl:444
[16] top-level scope
@ none:6
[17] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[18] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[19] _start()
@ Base ./client.jl:485
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/6lJsa/test/classification.jl:1
in expression starting at /home/pkgeval/.julia/packages/CAOS/6lJsa/test/runtests.jl:1
ERROR: Package CAOS errored during testing
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /buildworker/worker/package_linux64/build/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 /buildworker/worker/package_linux64/build/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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:331
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:318
[5] #test#62
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[6] test
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[7] #test#61
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[8] test
@ /buildworker/worker/package_linux64/build/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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[10] test(pkg::String)
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[11] top-level scope
@ none:31