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1.6.0-DEV-cbd854b0f4.log
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1.6.0-DEV-cbd854b0f4.log
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Julia Version 1.6.0-DEV.185
Commit cbd854b0f4 (2020-06-06 13:20 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-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed YAML ──────────────── v0.4.0
Installed Zlib_jll ──────────── v1.2.11+10
Installed Compat ────────────── v3.10.0
Installed TranscodingStreams ── v0.9.5
Installed OrderedCollections ── v1.2.0
Installed BufferedStreams ───── v1.0.0
Installed XAM ───────────────── v0.2.4
Installed BioSequences ──────── v2.0.4
Installed GenomicFeatures ───── v2.0.2
Installed Twiddle ───────────── v1.1.2
Installed CodecZlib ─────────── v0.7.0
Installed StableRNGs ────────── v0.1.1
Installed IndexableBitVectors ─ v1.0.0
Installed BioCore ───────────── v2.0.5
Installed DataStructures ────── v0.17.17
Installed BioSymbols ────────── v4.0.4
Installed BioAlignments ─────── v2.0.0
Installed BGZFStreams ───────── v0.3.0
Installed Indexes ───────────── v0.1.0
Installed IntervalTrees ─────── v1.0.0
Installed Combinatorics ─────── v1.0.2
Installed BioGenerics ───────── v0.1.0
Installed Automa ────────────── v0.8.0
Updating `~/.julia/environments/v1.6/Project.toml`
[d759349c] + XAM v0.2.4
Updating `~/.julia/environments/v1.6/Manifest.toml`
[67c07d97] + Automa v0.8.0
[28d598bf] + BGZFStreams v0.3.0
[00701ae9] + BioAlignments v2.0.0
[37cfa864] + BioCore v2.0.5
[47718e42] + BioGenerics v0.1.0
[7e6ae17a] + BioSequences v2.0.4
[3c28c6f8] + BioSymbols v4.0.4
[e1450e63] + BufferedStreams v1.0.0
[944b1d66] + CodecZlib v0.7.0
[861a8166] + Combinatorics v1.0.2
[34da2185] + Compat v3.10.0
[864edb3b] + DataStructures v0.17.17
[899a7d2d] + GenomicFeatures v2.0.2
[1cb3b9ac] + IndexableBitVectors v1.0.0
[4ffb77ac] + Indexes v0.1.0
[524e6230] + IntervalTrees v1.0.0
[bac558e1] + OrderedCollections v1.2.0
[860ef19b] + StableRNGs v0.1.1
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.2
[d759349c] + XAM v0.2.4
[ddb6d928] + YAML v0.4.0
[83775a58] + Zlib_jll v1.2.11+10
[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
Testing XAM
Status `/tmp/jl_3vcYGV/Project.toml`
[67c07d97] Automa v0.8.0
[28d598bf] BGZFStreams v0.3.0
[00701ae9] BioAlignments v2.0.0
[47718e42] BioGenerics v0.1.0
[7e6ae17a] BioSequences v2.0.4
[3372ea36] FormatSpecimens v1.0.1
[899a7d2d] GenomicFeatures v2.0.2
[4ffb77ac] Indexes v0.1.0
[3bb67fe8] TranscodingStreams v0.9.5
[d759349c] XAM v0.2.4
[de0858da] Printf
[8dfed614] Test
Status `/tmp/jl_3vcYGV/Manifest.toml`
[67c07d97] Automa v0.8.0
[28d598bf] BGZFStreams v0.3.0
[00701ae9] BioAlignments v2.0.0
[37cfa864] BioCore v2.0.5
[47718e42] BioGenerics v0.1.0
[7e6ae17a] BioSequences v2.0.4
[3c28c6f8] BioSymbols v4.0.4
[e1450e63] BufferedStreams v1.0.0
[944b1d66] CodecZlib v0.7.0
[861a8166] Combinatorics v1.0.2
[34da2185] Compat v3.10.0
[864edb3b] DataStructures v0.17.17
[3372ea36] FormatSpecimens v1.0.1
[899a7d2d] GenomicFeatures v2.0.2
[1cb3b9ac] IndexableBitVectors v1.0.0
[4ffb77ac] Indexes v0.1.0
[524e6230] IntervalTrees v1.0.0
[bac558e1] OrderedCollections v1.2.0
[860ef19b] StableRNGs v0.1.1
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.2
[d759349c] XAM v0.2.4
[ddb6d928] YAML v0.4.0
[83775a58] Zlib_jll v1.2.11+10
[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
[ 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}
Record: Error During Test at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:101
Test threw exception
Expression: SAM.sequence(record) == dna"TTAGATAAAGGATACTG"
UndefVarError: encode_copy! not defined
Stacktrace:
[1] sequence(::XAM.SAM.Record) at /home/pkgeval/.julia/packages/XAM/sS0E5/src/sam/record.jl:402
[2] top-level scope at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:101
[3] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1115
[4] top-level scope at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:71
[5] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1115
[6] top-level scope at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:26
Reader: Error During Test at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:123
Test threw exception
Expression: SAM.sequence(record) == sequence(record) == dna"CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
UndefVarError: encode_copy! not defined
Stacktrace:
[1] sequence(::XAM.SAM.Record) at /home/pkgeval/.julia/packages/XAM/sS0E5/src/sam/record.jl:402
[2] top-level scope at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:123
[3] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1115
[4] top-level scope at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:107
[5] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1115
[6] top-level scope at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:26
Test Summary: | Pass Error Total
SAM | 120 2 122
MetaInfo | 23 23
Header | 5 5
Record | 29 1 30
Reader | 28 1 29
Round trip | 28 28
In-Place-Reading Pattern | 7 7
ERROR: LoadError: Some tests did not pass: 120 passed, 0 failed, 2 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/XAM/sS0E5/test/runtests.jl:25
ERROR: Package XAM errored during testing
Stacktrace:
[1] pkgerror(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:52
[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/v1.6/Pkg/src/Operations.jl:1561
[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/v1.6/Pkg/src/API.jl:327
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:314
[5] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67 [inlined]
[6] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67 [inlined]
[7] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[8] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:66 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[10] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:65
[11] top-level scope at none:16