If you think that there is an error in how your package is being tested or represented, please file an issue at NewPkgEval.jl , making sure to read the FAQ first.
Results with Julia v1.2.0
Testing was unsuccessful : testing failed for unknown reasons.
Last evaluation was ago and took 17 minutes, 25 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed Missings ──────────────────── v0.4.3
Installed DataAPI ───────────────────── v1.1.0
Installed YAML ──────────────────────── v0.3.2
Installed TableTraits ───────────────── v1.0.0
Installed IntervalTrees ─────────────── v1.0.0
Installed CSV ───────────────────────── v0.5.18
Installed PhyloNetworks ─────────────── v0.11.0
Installed DataFrames ────────────────── v0.19.4
Installed ArrayLayouts ──────────────── v0.1.5
Installed StatsFuns ─────────────────── v0.9.0
Installed PDMats ────────────────────── v0.9.10
Installed Codecs ────────────────────── v0.5.0
Installed BioCore ───────────────────── v2.0.5
Installed BinaryProvider ────────────── v0.5.8
Installed IndexableBitVectors ───────── v1.0.0
Installed StatsBase ─────────────────── v0.32.0
Installed Polynomials ───────────────── v0.6.0
Installed DataValueInterfaces ───────── v1.0.0
Installed URIParser ─────────────────── v0.4.0
Installed PooledArrays ──────────────── v0.5.2
Installed Reexport ──────────────────── v0.2.0
Installed Twiddle ───────────────────── v1.1.1
Installed InvertedIndices ───────────── v1.0.0
Installed BioSymbols ────────────────── v3.1.0
Installed Compat ────────────────────── v2.2.0
Installed MathProgBase ──────────────── v0.7.7
Installed OrderedCollections ────────── v1.1.0
Installed Rmath ─────────────────────── v0.5.1
Installed Tables ────────────────────── v0.2.11
Installed FilePathsBase ─────────────── v0.7.0
Installed GLM ───────────────────────── v1.3.4
Installed Automa ────────────────────── v0.8.0
Installed DataStructures ────────────── v0.17.6
Installed RecipesBase ───────────────── v0.7.0
Installed WeakRefStrings ────────────── v0.6.1
Installed ShiftedArrays ─────────────── v1.0.0
Installed Distributions ─────────────── v0.21.9
Installed FillArrays ────────────────── v0.8.2
Installed StatsModels ───────────────── v0.6.7
Installed JSON ──────────────────────── v0.21.0
Installed Combinatorics ─────────────── v0.7.0
Installed Parameters ────────────────── v0.12.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed TranscodingStreams ────────── v0.9.5
Installed NLopt ─────────────────────── v0.5.1
Installed BioSequences ──────────────── v1.1.0
Installed StaticArrays ──────────────── v0.12.1
Installed QuadGK ────────────────────── v2.1.1
Installed Parsers ───────────────────── v0.3.10
Installed CategoricalArrays ─────────── v0.7.3
Installed CMake ─────────────────────── v1.1.2
Installed BufferedStreams ───────────── v1.0.0
Installed SortingAlgorithms ─────────── v0.3.1
Installed CMakeWrapper ──────────────── v0.2.3
Installed MacroTools ────────────────── v0.5.2
Installed BinDeps ───────────────────── v0.8.10
Installed Arpack ────────────────────── v0.3.1
Installed LazyArrays ────────────────── v0.14.10
Installed SpecialFunctions ──────────── v0.8.0
Updating `~/.julia/environments/v1.2/Project.toml`
[33ad39ac] + PhyloNetworks v0.11.0
Updating `~/.julia/environments/v1.2/Manifest.toml`
[7d9fca2a] + Arpack v0.3.1
[4c555306] + ArrayLayouts v0.1.5
[67c07d97] + Automa v0.8.0
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[37cfa864] + BioCore v2.0.5
[7e6ae17a] + BioSequences v1.1.0
[3c28c6f8] + BioSymbols v3.1.0
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[336ed68f] + CSV v0.5.18
[324d7699] + CategoricalArrays v0.7.3
[19ecbf4d] + Codecs v0.5.0
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.19.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.21.9
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[38e38edf] + GLM v1.3.4
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[5078a376] + LazyArrays v0.14.10
[1914dd2f] + MacroTools v0.5.2
[fdba3010] + MathProgBase v0.7.7
[e1d29d7a] + Missings v0.4.3
[76087f3c] + NLopt v0.5.1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[33ad39ac] + PhyloNetworks v0.11.0
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[1fd47b50] + QuadGK v2.1.1
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.5.1
[1277b4bf] + ShiftedArrays v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.0
[3eaba693] + StatsModels v0.6.7
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.1
[30578b45] + URIParser v0.4.0
[ea10d353] + WeakRefStrings v0.6.1
[ddb6d928] + YAML v0.3.2
[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
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Rmath ───────────→ `~/.julia/packages/Rmath/4wt82/deps/build.log`
Building CMake ───────────→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building NLopt ───────────→ `~/.julia/packages/NLopt/eqN9a/deps/build.log`
Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
Building Arpack ──────────→ `~/.julia/packages/Arpack/cu5By/deps/build.log`
Testing PhyloNetworks
Resolving package versions...
Status `/tmp/jl_KADugE/Manifest.toml`
[7d9fca2a] Arpack v0.3.1
[4c555306] ArrayLayouts v0.1.5
[67c07d97] Automa v0.8.0
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[37cfa864] BioCore v2.0.5
[7e6ae17a] BioSequences v1.1.0
[3c28c6f8] BioSymbols v3.1.0
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[336ed68f] CSV v0.5.18
[324d7699] CategoricalArrays v0.7.3
[19ecbf4d] Codecs v0.5.0
[861a8166] Combinatorics v0.7.0
[34da2185] Compat v2.2.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.19.4
[864edb3b] DataStructures v0.17.6
[e2d170a0] DataValueInterfaces v1.0.0
[31c24e10] Distributions v0.21.9
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.2
[38e38edf] GLM v1.3.4
[1cb3b9ac] IndexableBitVectors v1.0.0
[524e6230] IntervalTrees v1.0.0
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.0
[5078a376] LazyArrays v0.14.10
[1914dd2f] MacroTools v0.5.2
[fdba3010] MathProgBase v0.7.7
[e1d29d7a] Missings v0.4.3
[76087f3c] NLopt v0.5.1
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.10
[33ad39ac] PhyloNetworks v0.11.0
[f27b6e38] Polynomials v0.6.0
[2dfb63ee] PooledArrays v0.5.2
[1fd47b50] QuadGK v2.1.1
[3cdcf5f2] RecipesBase v0.7.0
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.5.1
[1277b4bf] ShiftedArrays v1.0.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.8.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.9.0
[3eaba693] StatsModels v0.6.7
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v0.2.11
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.1
[30578b45] URIParser v0.4.0
[ea10d353] WeakRefStrings v0.6.1
[ddb6d928] YAML v0.3.2
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
┌ Warning: PhyloNetworks.CHECKNET is true: will slow snaq! down.
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/auxiliary.jl:9
PhyloNetworks.CHECKNET = true
[ 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
[ Info: starting test_manipulateNet.jl
Test Summary: | Pass Total
test: move hybrid around cycle | 2 2
[1m[32mPASSED[0m: test_undirectedOtherNetworks.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
Test Summary: | Pass Total
testing rotate! | 2 2
[1m[32mPASSED[0m: test_manipulateNet.jl
[ Info: starting test_compareNetworks.jl
Test Summary: | Pass Total
test sets: compareNetworks | 84 84
[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
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 Total
multiple alleles | 22 22
[1m[32mPASSED[0m: test_multipleAlleles.jl
[ Info: starting test_bootstrap.jl
Test Summary: | Pass Total
testing hybridBootstrapSupport | 19 19
Test Summary: | Pass Total
bootsnaq from quartet CF intervals | 3 3
read 1/2 bootstrap tree files
read 2/2 bootstrap tree files
Test Summary: | Pass Total
bootsnaq from bootstrap gene trees, multiple procs | 18 18
[1m[32mPASSED[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_lm.jl
Test Summary: | Pass Total
phyloNetworklm on small network | 71 71
Shifts and Transgressive Evolution: Test Failed at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:206
Expression: table1.fstat[1] ≈ table2[2, :F]
Evaluated: NaN ≈ 46.84539027436086
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:206
[2] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Test/src/Test.jl:1113
[3] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Test Failed at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:207
Expression: table1.fstat[2] ≈ table2[1, :F]
Evaluated: 46.84539027436086 ≈ 0.0606956954548608
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:207
[2] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Test/src/Test.jl:1113
[3] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Error During Test at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:208
Test threw exception
Expression: (table1.pval[1]).v ≈ table2[2, Symbol("Pr(>F)")]
type Float64 has no field v
Stacktrace:
[1] getproperty(::Any, ::Symbol) at ./Base.jl:20
[2] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:208
[3] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Test/src/Test.jl:1113
[4] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Error During Test at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:209
Test threw exception
Expression: (table1.pval[2]).v ≈ table2[1, Symbol("Pr(>F)")]
type Float64 has no field v
Stacktrace:
[1] getproperty(::Any, ::Symbol) at ./Base.jl:20
[2] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:209
[3] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Test/src/Test.jl:1113
[4] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Test Summary: | Pass Fail Error Total
Shifts and Transgressive Evolution | 32 2 2 36
[1m[31mFAILED[0m: test_lm.jl
[ Info: starting test_lm_tree.jl
Test Summary: | Pass Total
phyloNetworklm: Caudata Dataset | 53 53
Test Summary: | Pass Total
phyloNetworklm: Lizard Dataset | 26 26
[1m[32mPASSED[0m: test_lm_tree.jl
[ Info: starting test_traits.jl
[ Info: starting test_simulate.jl
Test Summary: | Pass Total
traits: shared path, vcv, descendence matrix | 8 8
[1m[32mPASSED[0m: test_traits.jl
Test Summary: | Pass Total
Simulate function against fixed values | 4 4
Test Summary: | Pass Total
Simulate test distribution | 90 90
Test Summary: | Pass Total
Simulate with Shifts | 32 32
[1m[32mPASSED[0m: test_simulate.jl
[ Info: starting test_parsimony.jl
Test Summary: | Pass Total
Testing parsimony score & reconstruction | 38 38
Test Summary: | Pass Total
data from CSV, parsimony search | 1 1
[1m[32mPASSED[0m: test_parsimony.jl
[ Info: starting test_calibratePairwise.jl
Test Summary: | Pass Total
calibrate with distances: 3-cycle, non-identifiable example | 9 9
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
┌ Warning: the network contains taxa with no data: those will be pruned
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/traitsLikDiscrete.jl:681
┌ Warning: resetting edge numbers to be from 1 to 53
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/manipulateNet.jl:935
[ Info: starting test_readInputData.jl
Test Summary: | Pass Total
Testing traitLikDiscrete | 128 128
[1m[32mPASSED[0m: test_traitLikDiscrete.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%
***************
11 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged (ngenes too).
between 4.0 and 6.0 gene trees per 4-taxon set
Test Summary: | Pass Total
test: calculate quartet CF from input gene trees | 11 11
[ Info: starting test_nj.jl
[1m[32mPASSED[0m: test_readInputData.jl
Test Summary: | Pass Total
Neighbour joining implementation | 6 6
[1m[32mPASSED[0m: test_nj.jl
-------------------------------------
ERROR: LoadError: "Tests failed"
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/runtests.jl:112
[2] include at ./boot.jl:328 [inlined]
[3] include_relative(::Module, ::String) at ./loading.jl:1094
[4] include(::Module, ::String) at ./Base.jl:31
[5] include(::String) at ./client.jl:431
[6] top-level scope at none:5
in expression starting at /root/.julia/packages/PhyloNetworks/zeoh2/test/runtests.jl:111
ERROR: Package PhyloNetworks errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Types.jl:112
[2] #test#119(::Bool, ::Nothing, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Operations.jl:1288
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:245
[5] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:233 [inlined]
[6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
[7] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
[8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
[9] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
[11] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
[12] top-level scope at none:10
Results with Julia v1.3.0
Testing was unsuccessful : testing failed for unknown reasons.
Last evaluation was ago and took 21 minutes, 45 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed URIParser ─────────────────── v0.4.0
Installed SortingAlgorithms ─────────── v0.3.1
Installed YAML ──────────────────────── v0.3.2
Installed Arpack ────────────────────── v0.3.1
Installed BioSymbols ────────────────── v3.1.0
Installed DataStructures ────────────── v0.17.6
Installed LazyArrays ────────────────── v0.14.10
Installed PhyloNetworks ─────────────── v0.11.0
Installed StaticArrays ──────────────── v0.12.1
Installed Compat ────────────────────── v2.2.0
Installed BinaryProvider ────────────── v0.5.8
Installed QuadGK ────────────────────── v2.1.1
Installed StatsFuns ─────────────────── v0.9.0
Installed CategoricalArrays ─────────── v0.7.3
Installed InvertedIndices ───────────── v1.0.0
Installed Parsers ───────────────────── v0.3.10
Installed Combinatorics ─────────────── v0.7.0
Installed Missings ──────────────────── v0.4.3
Installed Distributions ─────────────── v0.21.9
Installed MacroTools ────────────────── v0.5.2
Installed Rmath ─────────────────────── v0.5.1
Installed IndexableBitVectors ───────── v1.0.0
Installed CSV ───────────────────────── v0.5.18
Installed NLopt ─────────────────────── v0.5.1
Installed CMakeWrapper ──────────────── v0.2.3
Installed TableTraits ───────────────── v1.0.0
Installed Parameters ────────────────── v0.12.0
Installed OrderedCollections ────────── v1.1.0
Installed SpecialFunctions ──────────── v0.8.0
Installed BioSequences ──────────────── v1.1.0
Installed ArrayLayouts ──────────────── v0.1.5
Installed BinDeps ───────────────────── v0.8.10
Installed JSON ──────────────────────── v0.21.0
Installed DataAPI ───────────────────── v1.1.0
Installed RecipesBase ───────────────── v0.7.0
Installed Codecs ────────────────────── v0.5.0
Installed Automa ────────────────────── v0.8.0
Installed Tables ────────────────────── v0.2.11
Installed ShiftedArrays ─────────────── v1.0.0
Installed DataValueInterfaces ───────── v1.0.0
Installed Polynomials ───────────────── v0.6.0
Installed IntervalTrees ─────────────── v1.0.0
Installed CMake ─────────────────────── v1.1.2
Installed StatsModels ───────────────── v0.6.7
Installed MathProgBase ──────────────── v0.7.7
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed GLM ───────────────────────── v1.3.4
Installed PooledArrays ──────────────── v0.5.2
Installed FilePathsBase ─────────────── v0.7.0
Installed Twiddle ───────────────────── v1.1.1
Installed WeakRefStrings ────────────── v0.6.1
Installed FillArrays ────────────────── v0.8.2
Installed Reexport ──────────────────── v0.2.0
Installed PDMats ────────────────────── v0.9.10
Installed TranscodingStreams ────────── v0.9.5
Installed BioCore ───────────────────── v2.0.5
Installed StatsBase ─────────────────── v0.32.0
Installed DataFrames ────────────────── v0.19.4
Installed BufferedStreams ───────────── v1.0.0
Updating `~/.julia/environments/v1.3/Project.toml`
[33ad39ac] + PhyloNetworks v0.11.0
Updating `~/.julia/environments/v1.3/Manifest.toml`
[7d9fca2a] + Arpack v0.3.1
[4c555306] + ArrayLayouts v0.1.5
[67c07d97] + Automa v0.8.0
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[37cfa864] + BioCore v2.0.5
[7e6ae17a] + BioSequences v1.1.0
[3c28c6f8] + BioSymbols v3.1.0
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[336ed68f] + CSV v0.5.18
[324d7699] + CategoricalArrays v0.7.3
[19ecbf4d] + Codecs v0.5.0
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.19.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.21.9
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[38e38edf] + GLM v1.3.4
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[5078a376] + LazyArrays v0.14.10
[1914dd2f] + MacroTools v0.5.2
[fdba3010] + MathProgBase v0.7.7
[e1d29d7a] + Missings v0.4.3
[76087f3c] + NLopt v0.5.1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[33ad39ac] + PhyloNetworks v0.11.0
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[1fd47b50] + QuadGK v2.1.1
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.5.1
[1277b4bf] + ShiftedArrays v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.0
[3eaba693] + StatsModels v0.6.7
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.1
[30578b45] + URIParser v0.4.0
[ea10d353] + WeakRefStrings v0.6.1
[ddb6d928] + YAML v0.3.2
[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
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Arpack ──────────→ `~/.julia/packages/Arpack/cu5By/deps/build.log`
Building Rmath ───────────→ `~/.julia/packages/Rmath/4wt82/deps/build.log`
Building CMake ───────────→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building NLopt ───────────→ `~/.julia/packages/NLopt/eqN9a/deps/build.log`
Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
Testing PhyloNetworks
Resolving package versions...
Status `/tmp/jl_xAAA3v/Manifest.toml`
[7d9fca2a] Arpack v0.3.1
[4c555306] ArrayLayouts v0.1.5
[67c07d97] Automa v0.8.0
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[37cfa864] BioCore v2.0.5
[7e6ae17a] BioSequences v1.1.0
[3c28c6f8] BioSymbols v3.1.0
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[336ed68f] CSV v0.5.18
[324d7699] CategoricalArrays v0.7.3
[19ecbf4d] Codecs v0.5.0
[861a8166] Combinatorics v0.7.0
[34da2185] Compat v2.2.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.19.4
[864edb3b] DataStructures v0.17.6
[e2d170a0] DataValueInterfaces v1.0.0
[31c24e10] Distributions v0.21.9
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.2
[38e38edf] GLM v1.3.4
[1cb3b9ac] IndexableBitVectors v1.0.0
[524e6230] IntervalTrees v1.0.0
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.0
[5078a376] LazyArrays v0.14.10
[1914dd2f] MacroTools v0.5.2
[fdba3010] MathProgBase v0.7.7
[e1d29d7a] Missings v0.4.3
[76087f3c] NLopt v0.5.1
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.10
[33ad39ac] PhyloNetworks v0.11.0
[f27b6e38] Polynomials v0.6.0
[2dfb63ee] PooledArrays v0.5.2
[1fd47b50] QuadGK v2.1.1
[3cdcf5f2] RecipesBase v0.7.0
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.5.1
[1277b4bf] ShiftedArrays v1.0.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.8.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.9.0
[3eaba693] StatsModels v0.6.7
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v0.2.11
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.1
[30578b45] URIParser v0.4.0
[ea10d353] WeakRefStrings v0.6.1
[ddb6d928] YAML v0.3.2
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
┌ Warning: PhyloNetworks.CHECKNET is true: will slow snaq! down.
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/auxiliary.jl:9
PhyloNetworks.CHECKNET = true
[ 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
[ Info: starting test_compareNetworks.jl
Test Summary: | Pass Total
testing rotate! | 2 2
[1m[32mPASSED[0m: test_manipulateNet.jl
Test Summary: | Pass Total
test sets: compareNetworks | 84 84
[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
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
[ Info: starting test_bootstrap.jl
Test Summary: | Pass Total
multiple alleles | 22 22
[1m[32mPASSED[0m: test_multipleAlleles.jl
Test Summary: | Pass Total
testing hybridBootstrapSupport | 19 19
Test Summary: | Pass Total
bootsnaq from quartet CF intervals | 3 3
read 1/2 bootstrap tree files
read 2/2 bootstrap tree files
Test Summary: | Pass Total
bootsnaq from bootstrap gene trees, multiple procs | 18 18
[1m[32mPASSED[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_lm.jl
Test Summary: | Pass Total
phyloNetworklm on small network | 71 71
Shifts and Transgressive Evolution: Test Failed at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:206
Expression: table1.fstat[1] ≈ table2[2, :F]
Evaluated: NaN ≈ 46.84539027436086
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:206
[2] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[3] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Test Failed at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:207
Expression: table1.fstat[2] ≈ table2[1, :F]
Evaluated: 46.84539027436086 ≈ 0.0606956954548608
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:207
[2] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[3] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Error During Test at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:208
Test threw exception
Expression: (table1.pval[1]).v ≈ table2[2, Symbol("Pr(>F)")]
type Float64 has no field v
Stacktrace:
[1] getproperty(::Float64, ::Symbol) at ./Base.jl:20
[2] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:208
[3] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[4] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Error During Test at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:209
Test threw exception
Expression: (table1.pval[2]).v ≈ table2[1, Symbol("Pr(>F)")]
type Float64 has no field v
Stacktrace:
[1] getproperty(::Float64, ::Symbol) at ./Base.jl:20
[2] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:209
[3] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[4] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Test Summary: | Pass Fail Error Total
Shifts and Transgressive Evolution | 32 2 2 36
[1m[31mFAILED[0m: test_lm.jl
[ Info: starting test_lm_tree.jl
Test Summary: | Pass Total
phyloNetworklm: Caudata Dataset | 53 53
Test Summary: | Pass Total
phyloNetworklm: Lizard Dataset | 26 26
[1m[32mPASSED[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 | 4 4
Test Summary: | Pass Total
Simulate test distribution | 90 90
[ Info: starting test_parsimony.jl
Test Summary: | Pass Total
Simulate with Shifts | 32 32
[1m[32mPASSED[0m: test_simulate.jl
Test Summary: | Pass Total
Testing parsimony score & reconstruction | 38 38
Test Summary: | Pass Total
data from CSV, parsimony search | 1 1
[1m[32mPASSED[0m: test_parsimony.jl
[ Info: starting test_calibratePairwise.jl
Test Summary: | Pass Total
calibrate with distances: 3-cycle, non-identifiable example | 9 9
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
┌ Warning: the network contains taxa with no data: those will be pruned
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/traitsLikDiscrete.jl:681
┌ Warning: resetting edge numbers to be from 1 to 53
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/manipulateNet.jl:935
[ Info: starting test_readInputData.jl
Test Summary: | Pass Total
Testing traitLikDiscrete | 128 128
[1m[32mPASSED[0m: test_traitLikDiscrete.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%
***************
11 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged (ngenes too).
between 4.0 and 6.0 gene trees per 4-taxon set
Test Summary: | Pass Total
test: calculate quartet CF from input gene trees | 11 11
[1m[32mPASSED[0m: test_readInputData.jl
[ Info: starting test_nj.jl
Test Summary: | Pass Total
Neighbour joining implementation | 6 6
[1m[32mPASSED[0m: test_nj.jl
-------------------------------------
ERROR: LoadError: "Tests failed"
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/runtests.jl:112
[2] include at ./boot.jl:328 [inlined]
[3] include_relative(::Module, ::String) at ./loading.jl:1105
[4] include(::Module, ::String) at ./Base.jl:31
[5] include(::String) at ./client.jl:424
[6] top-level scope at none:6
in expression starting at /root/.julia/packages/PhyloNetworks/zeoh2/test/runtests.jl:111
ERROR: Package PhyloNetworks errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:113
[2] #test#131(::Bool, ::Nothing, ::Cmd, ::Cmd, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Operations.jl:1370
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Cmd, ::Cmd, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:253
[5] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:239
[6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[7] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[9] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[11] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[12] top-level scope at none:10
Results with Julia v1.3.1-pre-7704df0a5a
Testing was unsuccessful : testing failed for unknown reasons.
Last evaluation was ago and took 22 minutes, 2 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed WeakRefStrings ────────────── v0.6.1
Installed ArrayLayouts ──────────────── v0.1.5
Installed CMake ─────────────────────── v1.1.2
Installed QuadGK ────────────────────── v2.1.1
Installed BioCore ───────────────────── v2.0.5
Installed DataStructures ────────────── v0.17.6
Installed Automa ────────────────────── v0.8.0
Installed PhyloNetworks ─────────────── v0.11.0
Installed Tables ────────────────────── v0.2.11
Installed NLopt ─────────────────────── v0.5.1
Installed SpecialFunctions ──────────── v0.8.0
Installed LazyArrays ────────────────── v0.14.10
Installed StatsModels ───────────────── v0.6.7
Installed Polynomials ───────────────── v0.6.0
Installed IntervalTrees ─────────────── v1.0.0
Installed DataFrames ────────────────── v0.19.4
Installed Compat ────────────────────── v2.2.0
Installed MacroTools ────────────────── v0.5.2
Installed BinDeps ───────────────────── v0.8.10
Installed StaticArrays ──────────────── v0.12.1
Installed FillArrays ────────────────── v0.8.2
Installed BufferedStreams ───────────── v1.0.0
Installed BioSymbols ────────────────── v3.1.0
Installed CMakeWrapper ──────────────── v0.2.3
Installed Arpack ────────────────────── v0.3.1
Installed StatsBase ─────────────────── v0.32.0
Installed Missings ──────────────────── v0.4.3
Installed URIParser ─────────────────── v0.4.0
Installed TableTraits ───────────────── v1.0.0
Installed ShiftedArrays ─────────────── v1.0.0
Installed PooledArrays ──────────────── v0.5.2
Installed StatsFuns ─────────────────── v0.9.0
Installed BinaryProvider ────────────── v0.5.8
Installed YAML ──────────────────────── v0.3.2
Installed FilePathsBase ─────────────── v0.7.0
Installed GLM ───────────────────────── v1.3.4
Installed Parameters ────────────────── v0.12.0
Installed TranscodingStreams ────────── v0.9.5
Installed Rmath ─────────────────────── v0.5.1
Installed InvertedIndices ───────────── v1.0.0
Installed Codecs ────────────────────── v0.5.0
Installed Twiddle ───────────────────── v1.1.1
Installed DataValueInterfaces ───────── v1.0.0
Installed Combinatorics ─────────────── v0.7.0
Installed MathProgBase ──────────────── v0.7.7
Installed Distributions ─────────────── v0.21.9
Installed RecipesBase ───────────────── v0.7.0
Installed CategoricalArrays ─────────── v0.7.3
Installed Reexport ──────────────────── v0.2.0
Installed DataAPI ───────────────────── v1.1.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed PDMats ────────────────────── v0.9.10
Installed OrderedCollections ────────── v1.1.0
Installed JSON ──────────────────────── v0.21.0
Installed Parsers ───────────────────── v0.3.10
Installed BioSequences ──────────────── v1.1.0
Installed CSV ───────────────────────── v0.5.18
Installed SortingAlgorithms ─────────── v0.3.1
Installed IndexableBitVectors ───────── v1.0.0
Updating `~/.julia/environments/v1.3/Project.toml`
[33ad39ac] + PhyloNetworks v0.11.0
Updating `~/.julia/environments/v1.3/Manifest.toml`
[7d9fca2a] + Arpack v0.3.1
[4c555306] + ArrayLayouts v0.1.5
[67c07d97] + Automa v0.8.0
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[37cfa864] + BioCore v2.0.5
[7e6ae17a] + BioSequences v1.1.0
[3c28c6f8] + BioSymbols v3.1.0
[e1450e63] + BufferedStreams v1.0.0
[631607c0] + CMake v1.1.2
[d5fb7624] + CMakeWrapper v0.2.3
[336ed68f] + CSV v0.5.18
[324d7699] + CategoricalArrays v0.7.3
[19ecbf4d] + Codecs v0.5.0
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.19.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.21.9
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[38e38edf] + GLM v1.3.4
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[5078a376] + LazyArrays v0.14.10
[1914dd2f] + MacroTools v0.5.2
[fdba3010] + MathProgBase v0.7.7
[e1d29d7a] + Missings v0.4.3
[76087f3c] + NLopt v0.5.1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.10
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[33ad39ac] + PhyloNetworks v0.11.0
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[1fd47b50] + QuadGK v2.1.1
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.5.1
[1277b4bf] + ShiftedArrays v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.0
[3eaba693] + StatsModels v0.6.7
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[3bb67fe8] + TranscodingStreams v0.9.5
[7200193e] + Twiddle v1.1.1
[30578b45] + URIParser v0.4.0
[ea10d353] + WeakRefStrings v0.6.1
[ddb6d928] + YAML v0.3.2
[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
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building CMake ───────────→ `~/.julia/packages/CMake/nSK2r/deps/build.log`
Building NLopt ───────────→ `~/.julia/packages/NLopt/eqN9a/deps/build.log`
Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
Building Arpack ──────────→ `~/.julia/packages/Arpack/cu5By/deps/build.log`
Building Rmath ───────────→ `~/.julia/packages/Rmath/4wt82/deps/build.log`
Testing PhyloNetworks
Resolving package versions...
Status `/tmp/jl_p5l3mb/Manifest.toml`
[7d9fca2a] Arpack v0.3.1
[4c555306] ArrayLayouts v0.1.5
[67c07d97] Automa v0.8.0
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[37cfa864] BioCore v2.0.5
[7e6ae17a] BioSequences v1.1.0
[3c28c6f8] BioSymbols v3.1.0
[e1450e63] BufferedStreams v1.0.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[336ed68f] CSV v0.5.18
[324d7699] CategoricalArrays v0.7.3
[19ecbf4d] Codecs v0.5.0
[861a8166] Combinatorics v0.7.0
[34da2185] Compat v2.2.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.19.4
[864edb3b] DataStructures v0.17.6
[e2d170a0] DataValueInterfaces v1.0.0
[31c24e10] Distributions v0.21.9
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.2
[38e38edf] GLM v1.3.4
[1cb3b9ac] IndexableBitVectors v1.0.0
[524e6230] IntervalTrees v1.0.0
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.0
[5078a376] LazyArrays v0.14.10
[1914dd2f] MacroTools v0.5.2
[fdba3010] MathProgBase v0.7.7
[e1d29d7a] Missings v0.4.3
[76087f3c] NLopt v0.5.1
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.10
[d96e819e] Parameters v0.12.0
[69de0a69] Parsers v0.3.10
[33ad39ac] PhyloNetworks v0.11.0
[f27b6e38] Polynomials v0.6.0
[2dfb63ee] PooledArrays v0.5.2
[1fd47b50] QuadGK v2.1.1
[3cdcf5f2] RecipesBase v0.7.0
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.5.1
[1277b4bf] ShiftedArrays v1.0.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.8.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.9.0
[3eaba693] StatsModels v0.6.7
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v0.2.11
[3bb67fe8] TranscodingStreams v0.9.5
[7200193e] Twiddle v1.1.1
[30578b45] URIParser v0.4.0
[ea10d353] WeakRefStrings v0.6.1
[ddb6d928] YAML v0.3.2
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[4607b0f0] SuiteSparse [`@stdlib/SuiteSparse`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
┌ Warning: PhyloNetworks.CHECKNET is true: will slow snaq! down.
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/auxiliary.jl:9
PhyloNetworks.CHECKNET = true
[ 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
[ Info: starting test_add2hyb.jl
Test Summary: | Pass Total
test: delete hybridization | 94 94
[1m[32mPASSED[0m: test_deleteHybridizationUpdate.jl
[ Info: starting test_optBLparts.jl
hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1
[1m[32mPASSED[0m: test_add2hyb.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
[ Info: starting test_undirectedOtherNetworks.jl
[1m[32mPASSED[0m: test_optBLparts.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
Test Summary: | Pass Total
testing rotate! | 2 2
[1m[32mPASSED[0m: test_manipulateNet.jl
[ Info: starting test_compareNetworks.jl
Test Summary: | Pass Total
test sets: compareNetworks | 84 84
[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
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 Total
multiple alleles | 22 22
[1m[32mPASSED[0m: test_multipleAlleles.jl
[ Info: starting test_bootstrap.jl
Test Summary: | Pass Total
testing hybridBootstrapSupport | 19 19
Test Summary: | Pass Total
bootsnaq from quartet CF intervals | 3 3
read 1/2 bootstrap tree files
read 2/2 bootstrap tree files
Test Summary: | Pass Total
bootsnaq from bootstrap gene trees, multiple procs | 18 18
[1m[32mPASSED[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_lm.jl
Test Summary: | Pass Total
phyloNetworklm on small network | 71 71
Shifts and Transgressive Evolution: Test Failed at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:206
Expression: table1.fstat[1] ≈ table2[2, :F]
Evaluated: NaN ≈ 46.84539027436086
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:206
[2] top-level scope at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[3] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Test Failed at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:207
Expression: table1.fstat[2] ≈ table2[1, :F]
Evaluated: 46.84539027436086 ≈ 0.0606956954548608
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:207
[2] top-level scope at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[3] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Error During Test at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:208
Test threw exception
Expression: (table1.pval[1]).v ≈ table2[2, Symbol("Pr(>F)")]
type Float64 has no field v
Stacktrace:
[1] getproperty(::Float64, ::Symbol) at ./Base.jl:20
[2] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:208
[3] top-level scope at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[4] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Shifts and Transgressive Evolution: Error During Test at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:209
Test threw exception
Expression: (table1.pval[2]).v ≈ table2[1, Symbol("Pr(>F)")]
type Float64 has no field v
Stacktrace:
[1] getproperty(::Float64, ::Symbol) at ./Base.jl:20
[2] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:209
[3] top-level scope at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Test/src/Test.jl:1107
[4] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/test_lm.jl:141
Test Summary: | Pass Fail Error Total
Shifts and Transgressive Evolution | 32 2 2 36
[1m[31mFAILED[0m: test_lm.jl
[ Info: starting test_lm_tree.jl
Test Summary: | Pass Total
phyloNetworklm: Caudata Dataset | 53 53
Test Summary: | Pass Total
phyloNetworklm: Lizard Dataset | 26 26
[1m[32mPASSED[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 | 4 4
Test Summary: | Pass Total
Simulate test distribution | 90 90
Test Summary: | Pass Total
Simulate with Shifts | 32 32
[1m[32mPASSED[0m: test_simulate.jl
[ Info: starting test_parsimony.jl
Test Summary: | Pass Total
Testing parsimony score & reconstruction | 38 38
Test Summary: | Pass Total
data from CSV, parsimony search | 1 1
[1m[32mPASSED[0m: test_parsimony.jl
[ Info: starting test_calibratePairwise.jl
Test Summary: | Pass Total
calibrate with distances: 3-cycle, non-identifiable example | 9 9
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
┌ Warning: the network contains taxa with no data: those will be pruned
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/traitsLikDiscrete.jl:681
┌ Warning: resetting edge numbers to be from 1 to 53
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/manipulateNet.jl:935
Test Summary: | Pass Total
Testing traitLikDiscrete | 128 128
[1m[32mPASSED[0m: test_traitLikDiscrete.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%
***************
11 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged (ngenes too).
between 4.0 and 6.0 gene trees per 4-taxon set
Test Summary: | Pass Total
test: calculate quartet CF from input gene trees | 11 11
[1m[32mPASSED[0m: test_readInputData.jl
[ Info: starting test_nj.jl
Test Summary: | Pass Total
Neighbour joining implementation | 6 6
[1m[32mPASSED[0m: test_nj.jl
-------------------------------------
ERROR: LoadError: "Tests failed"
Stacktrace:
[1] top-level scope at /root/.julia/packages/PhyloNetworks/zeoh2/test/runtests.jl:112
[2] include at ./boot.jl:328 [inlined]
[3] include_relative(::Module, ::String) at ./loading.jl:1105
[4] include(::Module, ::String) at ./Base.jl:31
[5] include(::String) at ./client.jl:424
[6] top-level scope at none:6
in expression starting at /root/.julia/packages/PhyloNetworks/zeoh2/test/runtests.jl:111
ERROR: Package PhyloNetworks errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:113
[2] #test#131(::Bool, ::Nothing, ::Cmd, ::Cmd, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/Operations.jl:1370
[3] #test at ./none:0 [inlined]
[4] #test#62(::Bool, ::Nothing, ::Cmd, ::Cmd, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:253
[5] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:239
[6] #test#61 at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[7] test at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:233 [inlined]
[8] #test#60 at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[9] test at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:232 [inlined]
[10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[11] test(::String) at /workspace/srcdir/julia/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:231
[12] top-level scope at none:10