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1.6.0-DEV-22b5d93b2b.log
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1.6.0-DEV-22b5d93b2b.log
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Julia Version 1.6.0-DEV.1069
Commit 22b5d93b2b (2020-09-28 17:33 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-10.0.1 (ORCJIT, skylake-avx512)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed OrderedCollections ── v1.3.1
Installed TranscodingStreams ── v0.9.5
Installed Twiddle ───────────── v1.1.2
Installed IntervalTrees ─────── v1.0.0
Installed Combinatorics ─────── v1.0.2
Installed BioGenerics ───────── v0.1.0
Installed StableRNGs ────────── v0.1.2
Installed BioAlignments ─────── v2.0.0
Installed BioSymbols ────────── v4.0.4
Installed DataStructures ────── v0.18.6
Installed Automa ────────────── v0.8.0
Installed Compat ────────────── v3.17.0
Installed IndexableBitVectors ─ v1.0.0
Installed BioSequences ──────── v2.0.5
Updating `~/.julia/environments/v1.6/Project.toml`
[00701ae9] + BioAlignments v2.0.0
Updating `~/.julia/environments/v1.6/Manifest.toml`
[67c07d97] + Automa v0.8.0
[00701ae9] + BioAlignments v2.0.0
[47718e42] + BioGenerics v0.1.0
[7e6ae17a] + BioSequences v2.0.5
[3c28c6f8] + BioSymbols v4.0.4
[861a8166] + Combinatorics v1.0.2
[34da2185] + Compat v3.17.0
[864edb3b] + DataStructures v0.18.6
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[bac558e1] + OrderedCollections v1.3.1
[860ef19b] + StableRNGs v0.1.2
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.2
[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 BioAlignments
Status `/tmp/jl_QaxMYL/Project.toml`
[00701ae9] BioAlignments v2.0.0
[47718e42] BioGenerics v0.1.0
[7e6ae17a] BioSequences v2.0.5
[3c28c6f8] BioSymbols v4.0.4
[524e6230] IntervalTrees v1.0.0
[37e2e46d] LinearAlgebra
[8dfed614] Test
Status `/tmp/jl_QaxMYL/Manifest.toml`
[67c07d97] Automa v0.8.0
[00701ae9] BioAlignments v2.0.0
[47718e42] BioGenerics v0.1.0
[7e6ae17a] BioSequences v2.0.5
[3c28c6f8] BioSymbols v4.0.4
[861a8166] Combinatorics v1.0.2
[34da2185] Compat v3.17.0
[864edb3b] DataStructures v0.18.6
[1cb3b9ac] IndexableBitVectors v1.0.0
[524e6230] IntervalTrees v1.0.0
[bac558e1] OrderedCollections v1.3.1
[860ef19b] StableRNGs v0.1.2
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.2
[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...
[ Info: Compiling bit-parallel GC counter for LongSequence{<:NucleicAcidAlphabet}
[ Info: Compiling bit-parallel mismatch counter for LongSequence{<:NucleicAcidAlphabet}
[ Info: Compiling bit-parallel match counter for LongSequence{<:NucleicAcidAlphabet}
[ Info: Compiling bit-parallel ambiguity counter...
[ Info: For a single LongSequence{<:NucleicAcidAlphabet}
[ Info: For a pair of LongSequence{<:NucleicAcidAlphabet}s
[ Info: Compiling bit-parallel certainty counter for LongSequence{<:NucleicAcidAlphabet}
[ Info: Compiling bit-parallel gap counter for LongSequence{<:NucleicAcidAlphabet}
Test Summary: | Pass Total
Alignments | 340 340
Print: Test Failed at /home/pkgeval/.julia/packages/BioAlignments/t4D8A/test/runtests.jl:980
Expression: sprint(show, aln) == "PairwiseAlignment{BioSequences.LongSequence{BioSequences.AminoAcidAlphabet},BioSequences.LongSequence{BioSequences.AminoAcidAlphabet}}:\n seq: 1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58\n || |||||||||||| |||| ||||||||||||| ||||||| |||||| |||| | |\n ref: 1 EP--SHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA 58\n"
Evaluated: "PairwiseAlignment{BioSequences.LongAminoAcidSeq, BioSequences.LongAminoAcidSeq}:\n seq: 1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58\n || |||||||||||| |||| ||||||||||||| ||||||| |||||| |||| | |\n ref: 1 EP--SHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA 58\n" == "PairwiseAlignment{BioSequences.LongSequence{BioSequences.AminoAcidAlphabet},BioSequences.LongSequence{BioSequences.AminoAcidAlphabet}}:\n seq: 1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58\n || |||||||||||| |||| ||||||||||||| ||||||| |||||| |||| | |\n ref: 1 EP--SHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA 58\n"
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/BioAlignments/t4D8A/test/runtests.jl:980
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/BioAlignments/t4D8A/test/runtests.jl:976
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/BioAlignments/t4D8A/test/runtests.jl:349
Test Summary: | Pass Fail Total
PairwiseAlignment | 226 1 227
SubstitutionMatrix | 28 28
AffineGapScoreModel | 25 25
CostModel | 11 11
Alignment | 5 5
count_<ops> | 5 5
Interfaces | 8 8
GlobalAlignment | 55 55
SemiGlobalAlignment | 12 12
OverlapAlignment | 15 15
LocalAlignment | 24 24
EditDistance | 22 22
LevenshteinDistance | 2 2
HammingDistance | 12 12
Print | 2 1 3
ERROR: LoadError: Some tests did not pass: 226 passed, 1 failed, 0 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/BioAlignments/t4D8A/test/runtests.jl:348
ERROR: Package BioAlignments errored during testing
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /workspace/srcdir/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 /workspace/srcdir/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 /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:331
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:318
[5] #test#62
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[6] test
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[7] #test#61
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[8] test
@ /workspace/srcdir/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 /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[10] test(pkg::String)
@ Pkg.API /workspace/srcdir/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[11] top-level scope
@ none:19