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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 InvertedIndices ────────────── v1.0.0
Installed Missings ───────────────────── v0.4.4
Installed QuadGK ─────────────────────── v2.4.1
Installed Automa ─────────────────────── v0.8.0
Installed StructTypes ────────────────── v1.1.0
Installed DataStructures ─────────────── v0.17.20
Installed FASTX ──────────────────────── v1.1.3
Installed PhyloNetworks ──────────────── v0.12.0
Installed NLopt_jll ──────────────────── v2.6.2+0
Installed GLM ────────────────────────── v1.3.10
Installed Compat ─────────────────────── v3.17.0
Installed TranscodingStreams ─────────── v0.9.5
Installed NLopt ──────────────────────── v0.6.0
Installed Twiddle ────────────────────── v1.1.2
Installed BioSequences ───────────────── v2.0.5
Installed Rmath_jll ──────────────────── v0.2.2+1
Installed SortingAlgorithms ──────────── v0.3.1
Installed ShiftedArrays ──────────────── v1.0.0
Installed Tables ─────────────────────── v1.0.5
Installed CompilerSupportLibraries_jll ─ v0.3.3+0
Installed Distributions ──────────────── v0.23.12
Installed SentinelArrays ─────────────── v1.2.15
Installed PDMats ─────────────────────── v0.10.1
Installed DataValueInterfaces ────────── v1.0.0
Installed PooledArrays ───────────────── v0.5.3
Installed CSV ────────────────────────── v0.7.7
Installed MathProgBase ───────────────── v0.7.8
Installed IndexableBitVectors ────────── v1.0.0
Installed TableTraits ────────────────── v1.0.0
Installed SpecialFunctions ───────────── v0.10.3
Installed Parsers ────────────────────── v1.0.10
Installed Reexport ───────────────────── v0.2.0
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed OrderedCollections ─────────── v1.3.1
Installed StatsModels ────────────────── v0.6.14
Installed DataAPI ────────────────────── v1.3.0
Installed StaticArrays ───────────────── v0.12.4
Installed StatsBase ──────────────────── v0.33.1
Installed JSON ───────────────────────── v0.21.1
Installed FillArrays ─────────────────── v0.9.6
Installed CategoricalArrays ──────────── v0.8.3
Installed StatsFuns ──────────────────── v0.9.5
Installed Combinatorics ──────────────── v1.0.2
Installed BioSymbols ─────────────────── v4.0.4
Installed Rmath ──────────────────────── v0.6.1
Installed IteratorInterfaceExtensions ── v1.0.0
Installed DataFrames ─────────────────── v0.21.7
Installed StableRNGs ─────────────────── v0.1.2
Installed BioGenerics ────────────────── v0.1.0
Updating `~/.julia/environments/v1.6/Project.toml`
[33ad39ac] + PhyloNetworks v0.12.0
Updating `~/.julia/environments/v1.6/Manifest.toml`
[67c07d97] + Automa v0.8.0
[47718e42] + BioGenerics v0.1.0
[7e6ae17a] + BioSequences v2.0.5
[3c28c6f8] + BioSymbols v4.0.4
[336ed68f] + CSV v0.7.7
[324d7699] + CategoricalArrays v0.8.3
[861a8166] + Combinatorics v1.0.2
[34da2185] + Compat v3.17.0
[e66e0078] + CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] + DataAPI v1.3.0
[a93c6f00] + DataFrames v0.21.7
[864edb3b] + DataStructures v0.17.20
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.23.12
[c2308a5c] + FASTX v1.1.3
[1a297f60] + FillArrays v0.9.6
[38e38edf] + GLM v1.3.10
[1cb3b9ac] + IndexableBitVectors v1.0.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.1
[fdba3010] + MathProgBase v0.7.8
[e1d29d7a] + Missings v0.4.4
[76087f3c] + NLopt v0.6.0
[079eb43e] + NLopt_jll v2.6.2+0
[efe28fd5] + OpenSpecFun_jll v0.5.3+3
[bac558e1] + OrderedCollections v1.3.1
[90014a1f] + PDMats v0.10.1
[69de0a69] + Parsers v1.0.10
[33ad39ac] + PhyloNetworks v0.12.0
[2dfb63ee] + PooledArrays v0.5.3
[1fd47b50] + QuadGK v2.4.1
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.1
[f50d1b31] + Rmath_jll v0.2.2+1
[91c51154] + SentinelArrays v1.2.15
[1277b4bf] + ShiftedArrays v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.10.3
[860ef19b] + StableRNGs v0.1.2
[90137ffa] + StaticArrays v0.12.4
[2913bbd2] + StatsBase v0.33.1
[4c63d2b9] + StatsFuns v0.9.5
[3eaba693] + StatsModels v0.6.14
[856f2bd8] + StructTypes v1.1.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v1.0.5
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.2
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[fa267f1f] + TOML
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Testing PhyloNetworks
Status `/tmp/jl_ilnutq/Project.toml`
[7e6ae17a] BioSequences v2.0.5
[3c28c6f8] BioSymbols v4.0.4
[336ed68f] CSV v0.7.7
[861a8166] Combinatorics v1.0.2
[a93c6f00] DataFrames v0.21.7
[864edb3b] DataStructures v0.17.20
[31c24e10] Distributions v0.23.12
[c2308a5c] FASTX v1.1.3
[38e38edf] GLM v1.3.10
[76087f3c] NLopt v0.6.0
[33ad39ac] PhyloNetworks v0.12.0
[90137ffa] StaticArrays v0.12.4
[2913bbd2] StatsBase v0.33.1
[4c63d2b9] StatsFuns v0.9.5
[3eaba693] StatsModels v0.6.14
[ade2ca70] Dates
[8ba89e20] Distributed
[37e2e46d] LinearAlgebra
[de0858da] Printf
[9a3f8284] Random
[10745b16] Statistics
[8dfed614] Test
Status `/tmp/jl_ilnutq/Manifest.toml`
[67c07d97] Automa v0.8.0
[47718e42] BioGenerics v0.1.0
[7e6ae17a] BioSequences v2.0.5
[3c28c6f8] BioSymbols v4.0.4
[336ed68f] CSV v0.7.7
[324d7699] CategoricalArrays v0.8.3
[861a8166] Combinatorics v1.0.2
[34da2185] Compat v3.17.0
[e66e0078] CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] DataAPI v1.3.0
[a93c6f00] DataFrames v0.21.7
[864edb3b] DataStructures v0.17.20
[e2d170a0] DataValueInterfaces v1.0.0
[31c24e10] Distributions v0.23.12
[c2308a5c] FASTX v1.1.3
[1a297f60] FillArrays v0.9.6
[38e38edf] GLM v1.3.10
[1cb3b9ac] IndexableBitVectors v1.0.0
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.1
[fdba3010] MathProgBase v0.7.8
[e1d29d7a] Missings v0.4.4
[76087f3c] NLopt v0.6.0
[079eb43e] NLopt_jll v2.6.2+0
[efe28fd5] OpenSpecFun_jll v0.5.3+3
[bac558e1] OrderedCollections v1.3.1
[90014a1f] PDMats v0.10.1
[69de0a69] Parsers v1.0.10
[33ad39ac] PhyloNetworks v0.12.0
[2dfb63ee] PooledArrays v0.5.3
[1fd47b50] QuadGK v2.4.1
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.6.1
[f50d1b31] Rmath_jll v0.2.2+1
[91c51154] SentinelArrays v1.2.15
[1277b4bf] ShiftedArrays v1.0.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.10.3
[860ef19b] StableRNGs v0.1.2
[90137ffa] StaticArrays v0.12.4
[2913bbd2] StatsBase v0.33.1
[4c63d2b9] StatsFuns v0.9.5
[3eaba693] StatsModels v0.6.14
[856f2bd8] StructTypes v1.1.0
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v1.0.5
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.2
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[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}
┌ Warning: PhyloNetworks.CHECKNET is true: will slow snaq! down.
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/CkmDl/src/auxiliary.jl:9
PhyloNetworks.CHECKNET = true
[ Info: starting test_auxillary.jl
Test Summary: | Pass Total
auxiliary | 24 24
[1m[32mPASSED[0m: test_auxillary.jl
[ Info: starting test_addHybrid.jl
Test Summary: | Pass Total
addhybridedge! top function | 11 11
Test Summary: | Pass Total
addhybridedge! helper function | 14 14
Test Summary: | Pass Total
edge checking functions | 11 11
[1m[32mPASSED[0m: test_addHybrid.jl
[ Info: starting test_5taxon_readTopology.jl
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 2 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_5taxon_readTopology.jl
[ Info: starting test_calculateExpCF.jl
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_calculateExpCF.jl
[ Info: starting test_calculateExpCF2.jl
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_calculateExpCF2.jl
[ Info: starting test_hasEdge.jl
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_hasEdge.jl
[ Info: starting test_parameters.jl
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 2 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_parameters.jl
[ Info: starting test_correctLik.jl
between 10.0 and 20.0 gene trees per 4-taxon set
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
Test Summary: | Pass Total
correct pseudo likelihood and snaq | 22 22
[1m[32mPASSED[0m: test_correctLik.jl
[ Info: starting test_partition.jl
[1m[32mPASSED[0m: test_partition.jl
[ Info: starting test_partition2.jl
Test Summary: | Pass Total
test: level-1 partitions | 53 53
[1m[32mPASSED[0m: test_partition2.jl
[ Info: starting test_deleteHybridizationUpdate.jl
Test Summary: | Pass Total
test: delete hybridization | 94 94
[1m[32mPASSED[0m: test_deleteHybridizationUpdate.jl
[ Info: starting test_add2hyb.jl
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_add2hyb.jl
[ Info: starting test_optBLparts.jl
hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_optBLparts.jl
[ Info: starting test_undirectedOtherNetworks.jl
Test Summary: | Pass Total
test: move hybrid around cycle | 2 2
[1m[32mPASSED[0m: test_undirectedOtherNetworks.jl
[ Info: starting test_manipulateNet.jl
Test Summary: | Pass Total
test: auxiliary | 27 27
RootMismatch: reverting to old root position.
Test Summary: | Pass Total
testing directEdges! and re-rootings | 20 20
Test Summary: | Pass Total
testing preorder! | 3 3
Test Summary: | Pass Total
testing cladewiseorder! | 2 2
WARNING: both LinearAlgebra and PhyloNetworks export "rotate!"; uses of it in module Main must be qualified
testing rotate!: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_manipulateNet.jl:202
Test threw exception
Expression: rotate!(net, -2, orderedEdgeNum = [1, 12, 9])
UndefVarError: rotate! not defined
Stacktrace:
[1] (::var"#300#303")()
@ Main ./none:0
[2] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:491
[3] with_logger
@ ./logging.jl:603 [inlined]
[4] #collect_test_logs#46
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:51 [inlined]
[5] collect_test_logs
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:50 [inlined]
[6] #match_logs#47
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:186 [inlined]
[7] match_logs(::Function)
@ Test /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:186
[8] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_manipulateNet.jl:202
[9] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[10] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_manipulateNet.jl:193
testing rotate!: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_manipulateNet.jl:203
Expression: [e.number for e = (net.node[12]).edge] == [1, 12, 9]
Evaluated: [1, 9, 12] == [1, 12, 9]
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_manipulateNet.jl:203
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_manipulateNet.jl:193
Test Summary: | Fail Error Total
testing rotate! | 1 1 2
[1m[31mFAILED[0m: test_manipulateNet.jl
[ Info: starting test_compareNetworks.jl
Test Summary: | Pass Total
test sets: compareNetworks | 109 109
[1m[32mPASSED[0m: test_compareNetworks.jl
[ Info: starting test_badDiamII.jl
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
Test Summary: | Pass Total
test: bad diamond, max pseudo lik | 23 23
[1m[32mPASSED[0m: test_badDiamII.jl
[ Info: starting test_multipleAlleles.jl
test: map alleles to species: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:14
Test threw exception
Expression: mapAllelesCFtable("tmp.csv", joinpath(#= /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:15 =# @__DIR__(), "..", "examples", "tableCFCI.csv"), filename = "CFmapped.csv")
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Bool, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] mapAllelesCFtable(alleleDF::String, cfDF::String; filename::String, columns::Vector{Int64}, CSVargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/CkmDl/src/multipleAlleles.jl:46
[9] (::var"#371#382")()
@ Main ./none:0
[10] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:491
[11] with_logger
@ ./logging.jl:603 [inlined]
[12] #collect_test_logs#46
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:51 [inlined]
[13] collect_test_logs
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:50 [inlined]
[14] #match_logs#47
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:186 [inlined]
[15] match_logs(f::Function, patterns::Tuple{Symbol, Regex})
@ Test /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:186
[16] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:14
[17] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[18] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:5
[19] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[20] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:2
test: map alleles to species: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:4
Got exception outside of a @test
IOError: unlink: no such file or directory (ENOENT)
Stacktrace:
[1] uv_error
@ ./libuv.jl:97 [inlined]
[2] unlink(p::String)
@ Base.Filesystem ./file.jl:916
[3] rm(path::String; force::Bool, recursive::Bool)
@ Base.Filesystem ./file.jl:270
[4] rm(path::String)
@ Base.Filesystem ./file.jl:261
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:18
[6] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[7] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:5
[8] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[9] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_multipleAlleles.jl:2
[10] include(fname::String)
@ Base.MainInclude ./client.jl:444
[11] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[12] include(fname::String)
@ Base.MainInclude ./client.jl:444
[13] top-level scope
@ none:6
[14] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[15] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[16] _start()
@ Base ./client.jl:485
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
11 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged.
hybrid edges for hybrid node 2 have missing gamma's, set default: 0.9,0.1
Test Summary: | Pass Error Total
multiple alleles | 20 2 22
test: map alleles to species | 2 2 4
sorttaxa! | 7 7
snaq on multiple alleles | 11 11
[1m[31mFAILED[0m: test_multipleAlleles.jl
[ Info: starting test_bootstrap.jl
Test Summary: | Pass Total
testing hybridBootstrapSupport | 19 19
bootsnaq from quartet CF intervals: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_bootstrap.jl:40
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_bootstrap.jl:42
[10] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[11] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_bootstrap.jl:41
[12] include(fname::String)
@ Base.MainInclude ./client.jl:444
[13] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[14] include(fname::String)
@ Base.MainInclude ./client.jl:444
[15] top-level scope
@ none:6
[16] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[17] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[18] _start()
@ Base ./client.jl:485
Test Summary: | Error Total
bootsnaq from quartet CF intervals | 1 1
[1m[31mFAILED[0m: test_bootstrap.jl
[ Info: starting test_perfectData.jl
hybrid edges for hybrid node 8 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 15 have missing gamma's, set default: 0.9,0.1
hybrid edges for hybrid node 4 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_perfectData.jl
[ Info: starting test_moves_semidirected.jl
Test Summary: | Pass Total
unconstrained NNI moves | 190 190
species constraints: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_moves_semidirected.jl:340
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] mapindividuals(net::HybridNetwork, mappingFile::String)
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/CkmDl/src/moves_semidirected.jl:778
[10] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_moves_semidirected.jl:388
[11] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[12] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_moves_semidirected.jl:341
[13] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[14] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_moves_semidirected.jl:340
[15] include(fname::String)
@ Base.MainInclude ./client.jl:444
[16] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[17] include(fname::String)
@ Base.MainInclude ./client.jl:444
[18] top-level scope
@ none:6
[19] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[20] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[21] _start()
@ Base ./client.jl:485
Test Summary: | Pass Error Total
constrained NNI moves | 29 1 30
species constraints | 19 1 20
test move root & constraint checking under species & clade constraints | 10 10
[1m[31mFAILED[0m: test_moves_semidirected.jl
[ Info: starting test_lm.jl
Test Summary: | Pass Total
phyloNetworklm on small network | 71 71
Test Summary: | Pass Total
Shifts and Transgressive Evolution | 36 36
Test Summary: | Pass Total
phyloNetworklm and ancestralStateReconstruction | 154 154
Test Summary: | Pass Total
lambda when no signal | 7 7
Test Summary: | Pass Total
phyloNetworklm with no regressor | 31 31
[1m[32mPASSED[0m: test_lm.jl
[ Info: starting test_lm_tree.jl
phyloNetworklm: Caudata Dataset: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_lm_tree.jl:6
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_lm_tree.jl:11
[10] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[11] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_lm_tree.jl:8
[12] include(fname::String)
@ Base.MainInclude ./client.jl:444
[13] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[14] include(fname::String)
@ Base.MainInclude ./client.jl:444
[15] top-level scope
@ none:6
[16] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[17] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[18] _start()
@ Base ./client.jl:485
Test Summary: | Error Total
phyloNetworklm: Caudata Dataset | 1 1
[1m[31mFAILED[0m: test_lm_tree.jl
[ Info: starting test_traits.jl
Test Summary: | Pass Total
traits: shared path, vcv, descendence matrix | 8 8
[1m[32mPASSED[0m: test_traits.jl
[ Info: starting test_simulate.jl
Test Summary: | Pass Total
Simulate function against fixed values | 5 5
Test Summary: | Pass Total
Simulate test distribution | 90 90
Test Summary: | Pass Total
Simulate with Shifts | 39 39
[1m[32mPASSED[0m: test_simulate.jl
[ Info: starting test_simulate_mbd.jl
Test Summary: | Pass Total
Simulate data and check means and dimensions | 8 8
Test Summary: | Pass Total
Simulate test distribution (fixed root) | 2 2
Test Summary: | Pass Total
Simulate test distribution (random root) | 3 3
Test Summary: | Pass Total
Simulate with Shifts | 22 22
[1m[32mPASSED[0m: test_simulate_mbd.jl
[ Info: starting test_parsimony.jl
Test Summary: | Pass Total
Testing parsimony score & reconstruction | 38 38
data from CSV, parsimony search: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_parsimony.jl:169
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_parsimony.jl:171
[10] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[11] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_parsimony.jl:170
[12] include(fname::String)
@ Base.MainInclude ./client.jl:444
[13] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[14] include(fname::String)
@ Base.MainInclude ./client.jl:444
[15] top-level scope
@ none:6
[16] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[17] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[18] _start()
@ Base ./client.jl:485
Test Summary: | Error Total
data from CSV, parsimony search | 1 1
[1m[31mFAILED[0m: test_parsimony.jl
[ Info: starting test_calibratePairwise.jl
Test Summary: | Pass Total
calibrate with distances: 3-cycle, non-identifiable example | 8 8
Test Summary: | Pass Total
calibrate with distances: 5-cycle example (when unrooted) | 8 8
[1m[32mPASSED[0m: test_calibratePairwise.jl
[ Info: starting test_relaxed_reading.jl
Test Summary: | Pass Total
test: newick parsing | 14 14
[1m[32mPASSED[0m: test_relaxed_reading.jl
[ Info: starting test_isMajor.jl
Test Summary: | Pass Total
readTopology Hybrid Node isMajor Tests | 11 11
Test Summary: | Pass Total
parsing extended newick | 6 6
[1m[32mPASSED[0m: test_isMajor.jl
[ Info: starting test_interop.jl
Test Summary: | Pass Total
testing interoperability, matrix-based net | 21 21
[1m[32mPASSED[0m: test_interop.jl
[ Info: starting test_traitLikDiscrete.jl
Testing random discrete trait simulation: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:109
Expression: a == [1 2 1 1 1 1 2]
Evaluated: [2 1 … 2 2] == [1 2 … 1 2]
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:109
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:98
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:3
Testing random discrete trait simulation: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:129
Expression: a == [1 1 1 2]
Evaluated: [1 1 2 1] == [1 1 1 2]
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:129
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:98
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:3
Testing random discrete trait simulation: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:133
Expression: a == [1 2 1 1 1 1 1 1 1]
Evaluated: [2 1 … 1 1] == [1 2 … 1 1]
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:133
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:98
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_traitLikDiscrete.jl:3
Test Summary: | Pass Fail Total
Testing traitLikDiscrete | 191 3 194
Testing Substitution Models, P and Q matrices | 17 17
types of RVAS | 43 43
Testing random discrete trait simulation | 5 3 8
Test discrete likelihood, fixed topology | 27 27
testing readfastatodna | 4 4
NucleicAcidSubsitutionModels | 13 13
fitdiscrete for NucleicAcidSubsitutionModels & RateVariationAcrossSites | 37 37
readfastatodna with NASM and RateVariationAcrossSites | 17 17
stationary and empiricalDNAfrequencies | 11 11
startingBL! | 6 6
testing prep and wrapper functions | 10 10
testing fit! functions for full network optimization | 1 1
[1m[31mFAILED[0m: test_traitLikDiscrete.jl
[ Info: starting test_phyLiNCoptimization.jl
optimizestructure with simple example: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:208
Expression: obj.loglik > -27.42
Evaluated: -28.26704053389549 > -27.42
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:208
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:194
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:3
optimizestructure with simple example: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:214
Expression: obj.loglik > -27.42
Evaluated: -28.26704053389549 > -27.42
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:214
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:194
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:3
phyLiNC no constraints: HKY, rate variation: Test Failed at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:245
Expression: obj.loglik > -27.27
Evaluated: -27.301530697290513 > -27.27
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:245
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:241
[4] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:3
phyLiNC with simple net and one constraint: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:272
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[9] mapindividuals(net::HybridNetwork, mappingFile::String)
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/CkmDl/src/moves_semidirected.jl:778
[10] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:276
[11] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[12] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:273
[13] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[14] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_phyLiNCoptimization.jl:3
[15] include(fname::String)
@ Base.MainInclude ./client.jl:444
[16] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[17] include(fname::String)
@ Base.MainInclude ./client.jl:444
[18] top-level scope
@ none:6
[19] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[20] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[21] _start()
@ Base ./client.jl:485
Test Summary: | Pass Fail Error Total
phyLiNC | 62 3 1 66
optimize local BL & gammas, simple example | 5 5
optimize local BL & gammas, complex network and 8 sites | 21 21
global branch length and gamma optimization | 5 5
data to SSM pruning: complex network | 5 5
checknetwork LiNC | 6 6
update root in SSM displayed trees | 3 3
skip γ and lengths optimization when needed | 5 5
optimizestructure with simple example | 1 2 3
phyLiNCone with simple net, no constraints | 4 4
phyLiNC no constraints: HKY, rate variation | 7 1 8
phyLiNC with simple net and one constraint | 1 1
[1m[31mFAILED[0m: test_phyLiNCoptimization.jl
[ Info: starting test_readInputData.jl
Test Summary: | Pass Total
test: reading nexus file | 6 6
Reading in trees, looking at 15 quartets in each...
0+------+100%
******
will use all quartets on 6 taxa
calculating obsCF from 6 gene trees and for 15 quartets
Reading in quartets...
0+---------------+100%
***************
test: calculate quartet CF from input gene trees: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_readInputData.jl:67
Test threw exception
Expression: mapAllelesCFtable("tmp_map.csv", "tmp_qCF.csv")
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Bool, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] mapAllelesCFtable(alleleDF::String, cfDF::String; filename::String, columns::Vector{Int64}, CSVargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ PhyloNetworks ~/.julia/packages/PhyloNetworks/CkmDl/src/multipleAlleles.jl:46
[9] mapAllelesCFtable
@ ~/.julia/packages/PhyloNetworks/CkmDl/src/multipleAlleles.jl:43 [inlined]
[10] (::var"#770#771")()
@ Main ./none:0
[11] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:491
[12] with_logger
@ ./logging.jl:603 [inlined]
[13] #collect_test_logs#46
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:51 [inlined]
[14] collect_test_logs
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:50 [inlined]
[15] #match_logs#47
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:186 [inlined]
[16] match_logs(f::Function, patterns::Tuple{Symbol, Regex})
@ Test /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:186
[17] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_readInputData.jl:67
[18] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[19] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_readInputData.jl:43
test: calculate quartet CF from input gene trees: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_readInputData.jl:42
Got exception outside of a @test
MethodError: no method matching readTableCF!(::Nothing)
Closest candidates are:
readTableCF!(!Matched::DataFrame; summaryfile) at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/src/readData.jl:101
readTableCF!(!Matched::DataFrame, !Matched::Vector{Int64}) at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/src/readData.jl:144
readTableCF!(!Matched::DataCF, !Matched::DataFrame, !Matched::Vector{Int64}) at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/src/readData.jl:197
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_readInputData.jl:69
[2] top-level scope
@ /workspace/srcdir/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1113
[3] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/test_readInputData.jl:43
[4] include(fname::String)
@ Base.MainInclude ./client.jl:444
[5] top-level scope
@ ~/.julia/packages/PhyloNetworks/CkmDl/test/runtests.jl:107
[6] include(fname::String)
@ Base.MainInclude ./client.jl:444
[7] top-level scope
@ none:6
[8] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[9] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[10] _start()
@ Base ./client.jl:485
Test Summary: | Pass Error Total
test: calculate quartet CF from input gene trees | 9 2 11
[1m[31mFAILED[0m: test_readInputData.jl
[ Info: starting test_nj.jl
Neighbour joining implementation: Error During Test at /home/pkgeval/.julia/packages/PhyloNetworks/CkmDl/test/test_nj.jl:1
Got exception outside of a @test
MethodError: no method matching typesubtract(::Type{Union{}}, ::Type{Int64})
Closest candidates are:
typesubtract(::Any, ::Any, !Matched::Int64) at compiler/typeutils.jl:66
Stacktrace:
[1] ts(T::Type, S::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:214
[2] nonstandardtype(T::Type)
@ CSV ~/.julia/packages/CSV/MKemC/src/utils.jl:217
[3] (::CSV.var"#17#23")(T::Type)
@ CSV ./none:0
[4] iterate(::Base.Iterators.Filter{CSV.var"#17#23", Vector{Type}})
@ Base.Iterators ./iterators.jl:451
[5] iterate
@ ./generator.jl:44 [inlined]
[6] Header
@ ~/.julia/packages/CSV/MKemC/src/header.jl:232 [inlined]
[7] CSV.File(source::String; header::Int64, normalizenames::Bool, datarow::Int64, skipto::Nothing, footerskip::Int64, transpose::Bool, comment::Nothing, use_mmap::Nothing, ignoreemptylines::Bool, select::Nothing, drop::Nothing, missingstrings::Vector{String}, missingstring::String, delim::Nothing, ignorerepeated::Bool, quotechar::Char, openquotechar::Nothing, closequotechar::Nothing, escapechar::Char, dateformat::Nothing, dateformats::Nothing, decimal::UInt8, truestrings::Vector{String}, falsestrings::Vector{String}, type::Nothing, types::Nothing, typemap::Dict{Type, Type}, categorical::Nothing, pool::Float64, lazystrings::Bool, strict::Bool, silencewarnings::Bool, debug::Bool, parsingdebug::Bool, kw::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}})
@ CSV ~/.julia/packages/CSV/MKemC/src/file.jl:216
[8] CSV.File(source::String)