Package evaluation of EcologicalNetworks on Julia 1.13.0-DEV.896 (efa4faf9a4*) started at 2025-07-25T13:36:01.608


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 14.13s


################################################################################
# Installation
#

Installing EcologicalNetworks...
   Resolving package versions...
   Installed HypergeometricFunctions ─ v0.3.28
   Installed Rmath_jll ─────────────── v0.5.1+0
   Installed AliasTables ───────────── v1.1.3
   Installed FillArrays ────────────── v1.13.0
   Installed DelimitedFiles ────────── v1.9.1
   Installed OrderedCollections ────── v1.8.1
   Installed Compat ────────────────── v4.17.0
   Installed DataAPI ───────────────── v1.16.0
   Installed DataStructures ────────── v0.18.22
   Installed Combinatorics ─────────── v1.0.3
   Installed StatsBase ─────────────── v0.33.21
   Installed StatsAPI ──────────────── v1.7.1
   Installed IrrationalConstants ───── v0.2.4
   Installed Statistics ────────────── v1.11.1
   Installed OpenSpecFun_jll ───────── v0.5.6+0
   Installed Requires ──────────────── v1.3.1
   Installed QuadGK ────────────────── v2.11.2
   Installed LogExpFunctions ───────── v0.3.29
   Installed PtrArrays ─────────────── v1.3.0
   Installed Rmath ─────────────────── v0.8.0
   Installed StatsFuns ─────────────── v1.5.0
   Installed Reexport ──────────────── v1.2.2
   Installed SpecialFunctions ──────── v2.5.1
   Installed Distributions ─────────── v0.25.120
   Installed EcologicalNetworks ────── v0.5.2
   Installed Preferences ───────────── v1.4.3
   Installed Missings ──────────────── v1.2.0
   Installed JLLWrappers ───────────── v1.7.1
   Installed PDMats ────────────────── v0.11.35
   Installed SortingAlgorithms ─────── v1.2.1
   Installed DocStringExtensions ───── v0.9.5
  Installing 2 artifacts
   Installed artifact Rmath       121.9 KiB
   Installed artifact OpenSpecFun 194.9 KiB
    Updating `~/.julia/environments/v1.13/Project.toml`
  [f03a62fe] + EcologicalNetworks v0.5.2
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [861a8166] + Combinatorics v1.0.3
  [34da2185] + Compat v4.17.0
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.18.22
  [8bb1440f] + DelimitedFiles v1.9.1
  [31c24e10] + Distributions v0.25.120
  [ffbed154] + DocStringExtensions v0.9.5
  [f03a62fe] + EcologicalNetworks v0.5.2
  [1a297f60] + FillArrays v1.13.0
  [34004b35] + HypergeometricFunctions v0.3.28
  [92d709cd] + IrrationalConstants v0.2.4
  [692b3bcd] + JLLWrappers v1.7.1
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.35
  [21216c6a] + Preferences v1.4.3
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [79098fc4] + Rmath v0.8.0
  [a2af1166] + SortingAlgorithms v1.2.1
  [276daf66] + SpecialFunctions v2.5.1
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
⌅ [2913bbd2] + StatsBase v0.33.21
  [4c63d2b9] + StatsFuns v1.5.0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.11.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.5+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [8e850b90] + libblastrampoline_jll v5.13.1+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 7.59s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...
Precompiling packages...
   3286.3 ms  ✓ TestEnv
  1 dependency successfully precompiled in 4 seconds. 26 already precompiled.

Precompiling package dependencies...

Precompilation completed after 106.6s


################################################################################
# Testing
#

     Testing EcologicalNetworks
      Status `/tmp/jl_R0WCpD/Project.toml`
  [f03a62fe] EcologicalNetworks v0.5.2
  [10745b16] Statistics v1.11.1
  [37e2e46d] LinearAlgebra v1.13.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_R0WCpD/Manifest.toml`
  [66dad0bd] AliasTables v1.1.3
  [861a8166] Combinatorics v1.0.3
  [34da2185] Compat v4.17.0
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.22
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.120
  [ffbed154] DocStringExtensions v0.9.5
  [f03a62fe] EcologicalNetworks v0.5.2
  [1a297f60] FillArrays v1.13.0
  [34004b35] HypergeometricFunctions v0.3.28
  [92d709cd] IrrationalConstants v0.2.4
  [692b3bcd] JLLWrappers v1.7.1
  [2ab3a3ac] LogExpFunctions v0.3.29
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.35
  [21216c6a] Preferences v1.4.3
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [79098fc4] Rmath v0.8.0
  [a2af1166] SortingAlgorithms v1.2.1
  [276daf66] SpecialFunctions v2.5.1
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
⌅ [2913bbd2] StatsBase v0.33.21
  [4c63d2b9] StatsFuns v1.5.0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.13.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [f489334b] StyledStrings v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.5+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [8e850b90] libblastrampoline_jll v5.13.1+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
Precompiling packages...
Info Given EcologicalNetworks was explicitly requested, output will be shown live 
WARNING: Method definition entropy(NT) where {NT<:EcologicalNetworks.AbstractEcologicalNetwork} in module EcologicalNetworks at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/src/information/entropy.jl:40 overwritten at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/src/information/entropy.jl:53.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
   5808.5 ms  ? EcologicalNetworks
WARNING: Method definition entropy(NT) where {NT<:EcologicalNetworks.AbstractEcologicalNetwork} in module EcologicalNetworks at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/src/information/entropy.jl:40 overwritten at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/src/information/entropy.jl:53.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
WARNING: Method definition entropy(NT) where {NT<:EcologicalNetworks.AbstractEcologicalNetwork} in module EcologicalNetworks at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/src/information/entropy.jl:40 overwritten at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/src/information/entropy.jl:53.
┌ Warning: Replacing docs for `EcologicalNetworks.entropy :: Tuple{NT} where NT<:EcologicalNetworks.AbstractEcologicalNetwork` in module `EcologicalNetworks`
└ @ Base.Docs docs/Docs.jl:253
[TEST  1] PASS types/declaration.jl
[TEST  2] PASS types/utilities.jl
[TEST  3] PASS types/conversions.jl
[TEST  4] PASS data.jl
[TEST  5] PASS links/degree.jl
[TEST  6] PASS links/specificity.jl
[TEST  7] PASS links/connectance.jl
[TEST  8] PASS links/degenerate.jl
[TEST  9] PASS rand/draws.jl
[TEST 10] PASS rand/shuffle.jl
[TEST 11] PASS rand/null.jl
[TEST 12] PASS rand/sample.jl
[TEST 13] PASS rand/cascademodel.jl
[TEST 14] PASS rand/nestedhierarchymodel.jl
[TEST 15] PASS rand/nichemodel.jl
[TEST 16] PASS rand/mpnmodel.jl
[TEST 17] PASS community/nestedness.jl
[TEST 18] PASS community/paths.jl
[TEST 19] PASS community/overlap.jl
[TEST 20] PASS community/centrality.jl
[TEST 21] PASS community/motifs.jl
[TEST 22] PASS community/foodwebs.jl
[TEST 23] PASS community/resilience.jl
[TEST 24] PASS community/spectralradius.jl
[TEST 25] FAIL betadiversity/operations.jl
LoadError: AssertionError: T == _species_type(N)
Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/EcologicalNetworks/pxEMG/test/runtests.jl:55
 [2] include(mapexpr::Function, mod::Module, _path::String)
   @ Base ./Base.jl:312
 [3] top-level scope
   @ none:6
 [4] eval(m::Module, e::Any)
   @ Core ./boot.jl:489
 [5] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:286
 [6] _start()
   @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/test/betadiversity/operations.jl:1
ERROR: LoadError: "TEST FAILED"
Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/EcologicalNetworks/pxEMG/test/runtests.jl:57
 [2] include(mapexpr::Function, mod::Module, _path::String)
   @ Base ./Base.jl:312
 [3] top-level scope
   @ none:6
 [4] eval(m::Module, e::Any)
   @ Core ./boot.jl:489
 [5] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:286
 [6] _start()
   @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/test/runtests.jl:48

caused by: LoadError: AssertionError: T == _species_type(N)
Stacktrace:
  [1] getindex(N::BipartiteNetwork{Bool, Symbol}, sp1::Vector{Any}, sp2::Vector{Any})
    @ EcologicalNetworks ~/.julia/packages/EcologicalNetworks/pxEMG/src/interfaces/abstractarray.jl:190
  [2] getindex(N::BipartiteNetwork{Bool, Symbol}, sp1::Vector{Symbol}, sp2::Vector{Symbol})
    @ EcologicalNetworks ~/.julia/packages/EcologicalNetworks/pxEMG/src/interfaces/abstractarray.jl:193
  [3] βos(X::BipartiteNetwork{Bool, Symbol}, Y::BipartiteNetwork{Bool, Symbol})
    @ EcologicalNetworks ~/.julia/packages/EcologicalNetworks/pxEMG/src/betadiversity/partitions.jl:40
  [4] top-level scope
    @ ~/.julia/packages/EcologicalNetworks/pxEMG/test/betadiversity/operations.jl:50
  [5] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:312
  [6] top-level scope
    @ ~/.julia/packages/EcologicalNetworks/pxEMG/test/runtests.jl:50
  [7] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:312
  [8] top-level scope
    @ none:6
  [9] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [10] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:286
 [11] _start()
    @ Base ./client.jl:553
in expression starting at /home/pkgeval/.julia/packages/EcologicalNetworks/pxEMG/test/betadiversity/operations.jl:1

Testing failed after 240.46s

ERROR: LoadError: Package EcologicalNetworks errored during testing
Stacktrace:
  [1] pkgerror(::String, ::Vararg{String})
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2661
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2510 [inlined]
  [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:538
  [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:311
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:320
 [12] _start()
    @ Base ./client.jl:553
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 389.29s: illegal method overwrites during precompilation