Circuitscape/Circuitscape.jl

pkg test failed

Closed this issue · 16 comments

tommydevitt commented

Can anyone tell me why the circuitscape package test is failing?

julia> Pkg.test("Circuitscape")
     Testing Circuitscape
      Status `/private/var/folders/yz/3xvfplr51n76z_803r4cv68dvwgqdt/T/jl_Sedyrg/Project.toml`
  [2169fc97] AlgebraicMultigrid v0.4.2
  [c9ce4bd3] ArchGDAL v0.7.4
  [2b7a1792] Circuitscape v5.10.2
  [92fee26a] GZip v0.5.1
  [86223c79] Graphs v1.7.0
  [42fd0dbc] IterativeSolvers v0.9.2
  [46dd5b70] Pardiso v0.5.4
  [47aef6b3] SimpleWeightedGraphs v1.2.1
  [ade2ca70] Dates `@stdlib/Dates`
  [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
  [8ba89e20] Distributed `@stdlib/Distributed`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [3fa0cd96] REPL `@stdlib/REPL`
  [1a1011a3] SharedArrays `@stdlib/SharedArrays`
  [2f01184e] SparseArrays `@stdlib/SparseArrays`
  [4607b0f0] SuiteSparse `@stdlib/SuiteSparse`
  [8dfed614] Test `@stdlib/Test`
      Status `/private/var/folders/yz/3xvfplr51n76z_803r4cv68dvwgqdt/T/jl_Sedyrg/Manifest.toml`
  [621f4979] AbstractFFTs v1.1.0
  [79e6a3ab] Adapt v3.3.3
  [2169fc97] AlgebraicMultigrid v0.4.2
  [c9ce4bd3] ArchGDAL v0.7.4
  [ec485272] ArnoldiMethod v0.2.0
  [fa961155] CEnum v0.4.2
  [d360d2e6] ChainRulesCore v1.15.0
  [9e997f8a] ChangesOfVariables v0.1.3
  [2b7a1792] Circuitscape v5.10.2
  [3da002f7] ColorTypes v0.11.3
  [c3611d14] ColorVectorSpace v0.9.9
  [5ae59095] Colors v0.12.8
  [34da2185] Compat v3.45.0
  [aa819f21] CompatHelper v3.3.0
  [9a962f9c] DataAPI v1.10.0
  [864edb3b] DataStructures v0.18.13
  [e2d170a0] DataValueInterfaces v1.0.0
  [3c3547ce] DiskArrays v0.2.13
  [ffbed154] DocStringExtensions v0.8.6
  [e2ba6199] ExprTools v0.1.8
  [53c48c17] FixedPointNumbers v0.8.4
  [add2ef01] GDAL v1.4.0
  [92fee26a] GZip v0.5.1
  [68eda718] GeoFormatTypes v0.3.0
  [cf35fbd7] GeoInterface v0.5.7
  [8f6bce27] GitForge v0.2.8
  [a2bd30eb] Graphics v1.1.2
  [86223c79] Graphs v1.7.0
  [cd3eb016] HTTP v0.9.17
  [a09fc81d] ImageCore v0.9.3
  [d25df0c9] Inflate v0.1.2
  [83e8ac13] IniFile v0.5.1
  [842dd82b] InlineStrings v1.1.2
  [3587e190] InverseFunctions v0.1.7
  [92d709cd] IrrationalConstants v0.1.1
  [42fd0dbc] IterativeSolvers v0.9.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.4.1
  [2535ab7d] JSON2 v0.3.4
  [2ab3a3ac] LogExpFunctions v0.3.15
  [1914dd2f] MacroTools v0.5.9
  [dbb5928d] MappedArrays v0.4.1
  [739be429] MbedTLS v1.0.3
  [78c3b35d] Mocking v0.7.3
  [e94cdb99] MosaicViews v0.3.3
  [1e8d2bf6] MultilineStrings v0.1.1
  [77ba4419] NaNMath v1.0.0
  [6fe1bfb0] OffsetArrays v1.12.5
  [bac558e1] OrderedCollections v1.4.1
  [5432bcbf] PaddedViews v0.5.11
  [46dd5b70] Pardiso v0.5.4
  [69de0a69] Parsers v2.3.1
  [21216c6a] Preferences v1.3.0
  [3cdcf5f2] RecipesBase v1.2.1
  [189a3867] Reexport v1.2.2
  [699a6c99] SimpleTraits v0.9.4
  [47aef6b3] SimpleWeightedGraphs v1.2.1
  [276daf66] SpecialFunctions v2.1.6
  [cae243ae] StackViews v0.1.1
  [90137ffa] StaticArrays v1.4.6
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.7.0
  [62fd8b95] TensorCore v0.1.1
  [f269a46b] TimeZones v1.7.3
  [5c2747f8] URIs v1.3.0
  [2e619515] Expat_jll v2.4.8+0
  [a7073274] GDAL_jll v300.500.0+1
  [d604d12d] GEOS_jll v3.10.2+0
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+2
  [aacddb02] JpegTurbo_jll v2.1.2+0
  [88015f11] LERC_jll v3.0.0+1
  [89763e89] Libtiff_jll v4.4.0+0
  [d3a379c0] LittleCMS_jll v2.12.0+0
  [856f044c] MKL_jll v2022.0.0+0
  [643b3616] OpenJpeg_jll v2.4.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [58948b4f] PROJ_jll v900.0.0+0
  [76ed43ae] SQLite_jll v3.38.4+0
  [3161d3a3] Zstd_jll v1.5.2+0
  [06c338fa] libgeotiff_jll v1.7.1+0
  [b53b4c65] libpng_jll v1.6.38+0
  [0dad84c5] ArgTools `@stdlib/ArgTools`
  [56f22d72] Artifacts `@stdlib/Artifacts`
  [2a0f44e3] Base64 `@stdlib/Base64`
  [ade2ca70] Dates `@stdlib/Dates`
  [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
  [8ba89e20] Distributed `@stdlib/Distributed`
  [f43a241f] Downloads `@stdlib/Downloads`
  [7b1f6079] FileWatching `@stdlib/FileWatching`
  [b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils`
  [4af54fe1] LazyArtifacts `@stdlib/LazyArtifacts`
  [b27032c2] LibCURL `@stdlib/LibCURL`
  [76f85450] LibGit2 `@stdlib/LibGit2`
  [8f399da3] Libdl `@stdlib/Libdl`
  [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
  [56ddb016] Logging `@stdlib/Logging`
  [d6f4376e] Markdown `@stdlib/Markdown`
  [a63ad114] Mmap `@stdlib/Mmap`
  [ca575930] NetworkOptions `@stdlib/NetworkOptions`
  [44cfe95a] Pkg `@stdlib/Pkg`
  [de0858da] Printf `@stdlib/Printf`
  [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`
  [fa267f1f] TOML `@stdlib/TOML`
  [a4e569a6] Tar `@stdlib/Tar`
  [8dfed614] Test `@stdlib/Test`
  [cf7118a7] UUIDs `@stdlib/UUIDs`
  [4ec0a83e] Unicode `@stdlib/Unicode`
  [e66e0078] CompilerSupportLibraries_jll `@stdlib/CompilerSupportLibraries_jll`
  [deac9b47] LibCURL_jll `@stdlib/LibCURL_jll`
  [29816b5a] LibSSH2_jll `@stdlib/LibSSH2_jll`
  [c8ffd9c3] MbedTLS_jll `@stdlib/MbedTLS_jll`
  [14a3606d] MozillaCACerts_jll `@stdlib/MozillaCACerts_jll`
  [4536629a] OpenBLAS_jll `@stdlib/OpenBLAS_jll`
  [05823500] OpenLibm_jll `@stdlib/OpenLibm_jll`
  [83775a58] Zlib_jll `@stdlib/Zlib_jll`
  [8e850b90] libblastrampoline_jll `@stdlib/libblastrampoline_jll`
  [8e850ede] nghttp2_jll `@stdlib/nghttp2_jll`
  [3f19e933] p7zip_jll `@stdlib/p7zip_jll`
     Testing Running tests...
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Circuitscape [2b7a1792-8151-5239-925d-e2b8fdfa3201]
│   exception = Required dependency ImageCore [a09fc81d-aa75-5fe9-8630-4744c3626534] failed to load from a cache file.
└ @ Base loading.jl:1132
pwd = /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test
Test Summary: | Pass  Total
Unit tests    |   16     16
ERROR: Package Circuitscape errored during testing (received signal: KILL)
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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 /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Operations.jl:1672
  [3] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:421
  [4] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
  [5] test(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
  [6] #test#87
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
  [7] test
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:142 [inlined]
  [8] #test#86
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:141 [inlined]
  [9] test(pkg::String)
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:141
 [10] top-level scope
    @ REPL[10]:1
ranjanan commented

Looks like something external is killing the test process?

tommydevitt commented

@ranjanan I'm not sure how to interpret the error, but looks like it has something to do with the required dependency "ImageCore" not loading? I ran Pkg.test("ImageCore") and got some warnings but ultimately "Testing ImageCore tests passed". Reran Pkg.test("Circuitscape") but still received "ERROR: Package Circuitscape errored during testing (received signal: KILL)".

ranjanan commented

Does It always error like:

ERROR: Package Circuitscape errored during testing (received signal: KILL)

Specifically, does it always say KILL? Could you be running out of memory and receiving a SIGKILL?

tommydevitt commented

So far that's all it says. I don't know whether it's running out of memory. Using a MacBook Air M1 chip with 16 GB RAM.

ranjanan commented

I just ran tests on an M2 MacBook Pro with 16 GB RAM using Rosetta and tests passed for me. I am not sure why the OS is killing your tests.

tommydevitt commented

Do I need to install Rosetta?

ranjanan commented

You already have Rosetta - that's how you were able to run the tests using Julia 1.7

tommydevitt commented

OK thanks. Anything else you can think of to try?

ranjanan commented

Yes, could you cd into your Circuitscape directory and run tests directly? So, open Julia, run:

using Circuitscape
normpath(joinpath(Base.pathof(Circuitscape), "..", "..", "test")) |> cd
include("runtests.jl")

and see what happens?

tommydevitt commented 
julia> include("runtests.jl")
pwd = /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test
Test Summary: | Pass  Total
Unit tests    |   16     16
Raster Pairwise: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:308
  Got exception outside of a @test
  Reordering problem.
  Stacktrace:
    [1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32)
      @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:80
    [2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64})
      @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:73
    [3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64})
      @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346
    [4] #_#36
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined]
    [5] MKLPardisoFactorize (repeats 2 times)
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined]
    [6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Matrix{Float64})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625
    [7] solve(prob::Circuitscape.GraphProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, solver::Circuitscape.MKLPardisoSolver, flags::Circuitscape.RasterFlags, cfg::Dict{String, String}, log::Bool)
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:445
    [8] single_ground_all_pairs (repeats 2 times)
      @ ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:66 [inlined]
    [9] _pt_file_no_polygons_path(rasterdata::Circuitscape.RasterData{Float64, Int64}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:63
   [10] raster_pairwise(T::Type, V::Type, cfg::Dict{String, String})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:29
   [11] _compute(T::Type, V::Type, cfg::Dict{String, String})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:43
   [12] macro expansion
      @ ./timing.jl:299 [inlined]
   [13] compute(path::String)
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31
   [14] macro expansion
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:317 [inlined]
   [15] macro expansion
      @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
   [16] macro expansion
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:310 [inlined]
   [17] macro expansion
      @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
   [18] runtests(f::typeof(compute))
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278
   [19] top-level scope
      @ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16
   [20] include(fname::String)
      @ Base.MainInclude ./client.jl:451
   [21] top-level scope
      @ REPL[3]:1
   [22] eval
      @ ./boot.jl:373 [inlined]
   [23] eval_user_input(ast::Any, backend::REPL.REPLBackend)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
   [24] repl_backend_loop(backend::REPL.REPLBackend)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
   [25] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
   [26] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
   [27] run_repl(repl::REPL.AbstractREPL, consumer::Any)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
   [28] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module)
      @ Base ./client.jl:394
   [29] #invokelatest#2
      @ ./essentials.jl:716 [inlined]
   [30] invokelatest
      @ ./essentials.jl:714 [inlined]
   [31] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
      @ Base ./client.jl:379
   [32] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:309
   [33] _start()
      @ Base ./client.jl:495
Raster Advanced: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:328
  Got exception outside of a @test
  Reordering problem.
  Stacktrace:
    [1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32)
      @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:80
    [2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64})
      @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:73
    [3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64})
      @ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346
    [4] #_#36
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined]
    [5] MKLPardisoFactorize (repeats 2 times)
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined]
    [6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Vector{Float64})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625
    [7] macro expansion
      @ ./timing.jl:299 [inlined]
    [8] multiple_solve(s::Circuitscape.MKLPardisoSolver, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, suppress_info::Bool)
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:330
    [9] multiple_solver(cfg::Dict{String, String}, solver::Circuitscape.MKLPardisoSolver, a::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, grounds::Vector{Float64}, finitegrounds::Vector{Float64})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:292
   [10] advanced_kernel(prob::Circuitscape.AdvancedProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:205
   [11] raster_advanced(T::Type, V::Type, cfg::Dict{String, String})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:30
   [12] _compute(T::Type, V::Type, cfg::Dict{String, String})
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:45
   [13] macro expansion
      @ ./timing.jl:299 [inlined]
   [14] compute(path::String)
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31
   [15] macro expansion
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:332 [inlined]
   [16] macro expansion
      @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
   [17] macro expansion
      @ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:330 [inlined]
   [18] macro expansion
      @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
   [19] runtests(f::typeof(compute))
      @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278
   [20] top-level scope
      @ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16
   [21] include(fname::String)
      @ Base.MainInclude ./client.jl:451
   [22] top-level scope
      @ REPL[3]:1
   [23] eval
      @ ./boot.jl:373 [inlined]
   [24] eval_user_input(ast::Any, backend::REPL.REPLBackend)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
   [25] repl_backend_loop(backend::REPL.REPLBackend)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
   [26] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
   [27] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
   [28] run_repl(repl::REPL.AbstractREPL, consumer::Any)
      @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
   [29] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module)
      @ Base ./client.jl:394
   [30] #invokelatest#2
      @ ./essentials.jl:716 [inlined]
   [31] invokelatest
      @ ./essentials.jl:714 [inlined]
   [32] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
      @ Base ./client.jl:379
   [33] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:309
   [34] _start()
      @ Base ./client.jl:495
      From worker 2:	[ Info: 2022-07-08 21:32:08 : Solving point 1 of 10
      From worker 3:	[ Info: 2022-07-08 21:32:08 : Solving point 2 of 10
      From worker 3:	[ Info: 2022-07-08 21:32:08 : Solver used: AMG accelerated by CG
      From worker 2:	[ Info: 2022-07-08 21:32:08 : Solver used: AMG accelerated by CG
      From worker 2:	[ Info: 2022-07-08 21:32:13 : Time taken to construct preconditioner = 1.177736791 seconds
      From worker 2:	[ Info: 2022-07-08 21:32:13 : Time taken to solve linear system = 0.004022333 seconds
      From worker 3:	[ Info: 2022-07-08 21:32:13 : Time taken to construct preconditioner = 1.237418583 seconds
      From worker 3:	[ Info: 2022-07-08 21:32:13 : Time taken to solve linear system = 0.004103167 seconds
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solving point 3 of 10
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solving point 4 of 10
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solving point 5 of 10
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 0.0002465 seconds
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 8.8125e-5 seconds
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 0.000197209 seconds
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 8.575e-5 seconds
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solving point 6 of 10
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solving point 7 of 10
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 7.3584e-5 seconds
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 7.2042e-5 seconds
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solving point 8 of 10
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Time taken to construct preconditioner = 8.325e-5 seconds
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Time taken to solve linear system = 7.3958e-5 seconds
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solving point 9 of 10
      From worker 3:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solving point 10 of 10
      From worker 2:	[ Info: 2022-07-08 21:32:14 : Solver used: AMG accelerated by CG
      From worker 5:	[ Info: 2022-07-08 21:32:25 : Solving point 1 of 5
      From worker 4:	[ Info: 2022-07-08 21:32:25 : Solving point 2 of 5
      From worker 5:	[ Info: 2022-07-08 21:32:26 : Solver used: AMG accelerated by CG
      From worker 4:	[ Info: 2022-07-08 21:32:26 : Solver used: AMG accelerated by CG
      From worker 4:	[ Info: 2022-07-08 21:32:30 : Time taken to construct preconditioner = 1.146539792 seconds
      From worker 5:	[ Info: 2022-07-08 21:32:30 : Time taken to construct preconditioner = 1.16853475 seconds
      From worker 5:	[ Info: 2022-07-08 21:32:30 : Time taken to solve linear system = 0.003904917 seconds
      From worker 4:	[ Info: 2022-07-08 21:32:30 : Time taken to solve linear system = 0.00410575 seconds
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Solving point 3 of 5
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Solver used: AMG accelerated by CG
      From worker 5:	[ Info: 2022-07-08 21:32:31 : Solving point 4 of 5
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Time taken to construct preconditioner = 9.1167e-5 seconds
      From worker 5:	[ Info: 2022-07-08 21:32:31 : Solver used: AMG accelerated by CG
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Time taken to solve linear system = 1.8625e-5 seconds
      From worker 5:	[ Info: 2022-07-08 21:32:31 : Time taken to construct preconditioner = 7.2041e-5 seconds
      From worker 5:	[ Info: 2022-07-08 21:32:31 : Time taken to solve linear system = 1.75e-5 seconds
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Solving point 5 of 5
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Solver used: AMG accelerated by CG
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Time taken to construct preconditioner = 4.1167e-5 seconds
      From worker 4:	[ Info: 2022-07-08 21:32:31 : Time taken to solve linear system = 9.833e-6 seconds
┌ Warning: 2022-07-08 21:32:31 : Code to include pairs is activated, some entries did not match with focal node file. Some focal nodes may have been dropped
└ @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/logging.jl:25
Test Summary:          | Pass  Error  Total
Double Precision Tests |  383      2    385
  Network Pairwise     |  141           141
  Network Advanced     |   12            12
  Raster Pairwise      |           1      1
  Raster Advanced      |           1      1
  Raster One to All    |  134           134
  Raster All to One    |   96            96
ERROR: LoadError: Some tests did not pass: 383 passed, 0 failed, 2 errored, 0 broken.
in expression starting at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:15
ranjanan commented

okay, at least you didn't get the kill. One last thing. Can you run using Pkg; Pkg.update() and then run the tests again? I notice you're on a slightly older version of Circuitscape.

tommydevitt commented

OK, did that, but same (?) result:

julia> include("runtests.jl")
ERROR: SystemError: opening file "/Users/tjd66/runtests.jl": No such file or directory
Stacktrace:
[1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
@ Base ./error.jl:174
[2] #systemerror#68
@ ./error.jl:173 [inlined]
[3] systemerror
@ ./error.jl:173 [inlined]
[4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
@ Base ./iostream.jl:293
[5] open
@ ./iostream.jl:282 [inlined]
[6] open(f::Base.var"#364#365"{String}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Base ./io.jl:328
[7] open
@ ./io.jl:328 [inlined]
[8] read
@ ./io.jl:436 [inlined]
[9] _include(mapexpr::Function, mod::Module, _path::String)
@ Base ./loading.jl:1249
[10] include(fname::String)
@ Base.MainInclude ./client.jl:451
[11] top-level scope
@ REPL[4]:1

julia> normpath(joinpath(Base.pathof(Circuitscape), "..", "..", "test")) |> cd

julia> using Circuitscape

julia> normpath(joinpath(Base.pathof(Circuitscape), "..", "..", "test")) |> cd

julia> include("runtests.jl")
pwd = /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test
Test Summary: | Pass Total
Unit tests | 16 16
Raster Pairwise: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:308
Got exception outside of a @test
Reordering problem.
Stacktrace:
[1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32)
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:80
[2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:73
[3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346
[4] #_#36
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined]
[5] MKLPardisoFactorize (repeats 2 times)
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined]
[6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Matrix{Float64})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625
[7] solve(prob::Circuitscape.GraphProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, solver::Circuitscape.MKLPardisoSolver, flags::Circuitscape.RasterFlags, cfg::Dict{String, String}, log::Bool)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:445
[8] single_ground_all_pairs (repeats 2 times)
@ ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:66 [inlined]
[9] _pt_file_no_polygons_path(rasterdata::Circuitscape.RasterData{Float64, Int64}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:63
[10] raster_pairwise(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/pairwise.jl:29
[11] _compute(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:43
[12] macro expansion
@ ./timing.jl:299 [inlined]
[13] compute(path::String)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31
[14] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:317 [inlined]
[15] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[16] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:310 [inlined]
[17] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[18] runtests(f::typeof(compute))
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278
[19] top-level scope
@ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16
[20] include(fname::String)
@ Base.MainInclude ./client.jl:451
[21] top-level scope
@ REPL[8]:1
[22] eval
@ ./boot.jl:373 [inlined]
[23] eval_user_input(ast::Any, backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
[24] repl_backend_loop(backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
[25] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
[26] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
[27] run_repl(repl::REPL.AbstractREPL, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
[28] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module)
@ Base ./client.jl:394
[29] #invokelatest#2
@ ./essentials.jl:716 [inlined]
[30] invokelatest
@ ./essentials.jl:714 [inlined]
[31] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
@ Base ./client.jl:379
[32] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:309
[33] start()
@ Base ./client.jl:495
Raster Advanced: Error During Test at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/src/utils.jl:328
Got exception outside of a @test
Not enough memory.
Stacktrace:
[1] check_error(ps::Pardiso.MKLPardisoSolver, err::Int32)
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:79
[2] ccall_pardiso(ps::Pardiso.MKLPardisoSolver, N::Int64, nzval::Vector{Float64}, colptr::Vector{Int64}, rowval::Vector{Int64}, NRHS::Int64, B::Vector{Float64}, X::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/mkl_pardiso.jl:73
[3] pardiso(ps::Pardiso.MKLPardisoSolver, X::Vector{Float64}, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, B::Vector{Float64})
@ Pardiso ~/.julia/packages/Pardiso/rrIt7/src/Pardiso.jl:346
[4] ##36
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:459 [inlined]
[5] MKLPardisoFactorize (repeats 2 times)
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:457 [inlined]
[6] solve_linear_system(factor::Circuitscape.MKLPardisoFactorize, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, rhs::Vector{Float64})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/core.jl:625
[7] macro expansion
@ ./timing.jl:299 [inlined]
[8] multiple_solve(s::Circuitscape.MKLPardisoSolver, matrix::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, suppress_info::Bool)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:330
[9] multiple_solver(cfg::Dict{String, String}, solver::Circuitscape.MKLPardisoSolver, a::SparseArrays.SparseMatrixCSC{Float64, Int64}, sources::Vector{Float64}, grounds::Vector{Float64}, finitegrounds::Vector{Float64})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:292
[10] advanced_kernel(prob::Circuitscape.AdvancedProblem{Float64, Int64, Circuitscape.MKLPardisoSolver}, flags::Circuitscape.RasterFlags, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:205
[11] raster_advanced(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/raster/advanced.jl:30
[12] _compute(T::Type, V::Type, cfg::Dict{String, String})
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:45
[13] macro expansion
@ ./timing.jl:299 [inlined]
[14] compute(path::String)
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/run.jl:31
[15] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:332 [inlined]
[16] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[17] macro expansion
@ ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:330 [inlined]
[18] macro expansion
@ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined]
[19] runtests(f::typeof(compute))
@ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/utils.jl:278
[20] top-level scope
@ ~/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:16
[21] include(fname::String)
@ Base.MainInclude ./client.jl:451
[22] top-level scope
@ REPL[8]:1
[23] eval
@ ./boot.jl:373 [inlined]
[24] eval_user_input(ast::Any, backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
[25] repl_backend_loop(backend::REPL.REPLBackend)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
[26] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
[27] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
[28] run_repl(repl::REPL.AbstractREPL, consumer::Any)
@ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
[29] (::Base.var"#936#938"{Bool, Bool, Bool})(REPL::Module)
@ Base ./client.jl:394
[30] #invokelatest#2
@ ./essentials.jl:716 [inlined]
[31] invokelatest
@ ./essentials.jl:714 [inlined]
[32] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
@ Base ./client.jl:379
[33] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:309
[34] _start()
@ Base ./client.jl:495
From worker 3: [ Info: 2022-07-08 23:16:03 : Solving point 2 of 10
From worker 2: [ Info: 2022-07-08 23:16:03 : Solving point 1 of 10
From worker 3: [ Info: 2022-07-08 23:16:04 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 23:16:04 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:08 : Time taken to construct preconditioner = 1.206053834 seconds
From worker 3: [ Info: 2022-07-08 23:16:08 : Time taken to solve linear system = 0.004389292 seconds
From worker 2: [ Info: 2022-07-08 23:16:08 : Time taken to construct preconditioner = 1.176347083 seconds
From worker 2: [ Info: 2022-07-08 23:16:08 : Time taken to solve linear system = 0.003827583 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 3 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 4 of 10
From worker 2: [ Info: 2022-07-08 23:16:09 : Solving point 5 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 0.000268542 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 9.85e-5 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 6 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 7 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 9.9167e-5 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 7.7625e-5 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 8 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 6.6834e-5 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 7.5791e-5 seconds
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 9 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 3: [ Info: 2022-07-08 23:16:09 : Solving point 10 of 10
From worker 3: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 23:16:09 : Solver used: AMG accelerated by CG
From worker 2: [ Info: 2022-07-08 23:16:09 : Time taken to construct preconditioner = 0.000213708 seconds
From worker 2: [ Info: 2022-07-08 23:16:09 : Time taken to solve linear system = 9.15e-5 seconds
From worker 5: [ Info: 2022-07-08 23:16:20 : Solving point 2 of 5
From worker 4: [ Info: 2022-07-08 23:16:20 : Solving point 1 of 5
From worker 5: [ Info: 2022-07-08 23:16:21 : Solver used: AMG accelerated by CG
From worker 4: [ Info: 2022-07-08 23:16:21 : Solver used: AMG accelerated by CG
From worker 5: [ Info: 2022-07-08 23:16:25 : Time taken to construct preconditioner = 1.214680958 seconds
From worker 5: [ Info: 2022-07-08 23:16:25 : Time taken to solve linear system = 0.004146291 seconds
From worker 4: [ Info: 2022-07-08 23:16:25 : Time taken to construct preconditioner = 1.173361292 seconds
From worker 4: [ Info: 2022-07-08 23:16:25 : Time taken to solve linear system = 0.00401875 seconds
From worker 5: [ Info: 2022-07-08 23:16:26 : Solving point 3 of 5
From worker 5: [ Info: 2022-07-08 23:16:26 : Solver used: AMG accelerated by CG
From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to construct preconditioner = 9.0541e-5 seconds
From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to solve linear system = 1.7084e-5 seconds
From worker 5: [ Info: 2022-07-08 23:16:26 : Solving point 4 of 5
From worker 5: [ Info: 2022-07-08 23:16:26 : Solver used: AMG accelerated by CG
From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to construct preconditioner = 3.2833e-5 seconds
From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to solve linear system = 1.2666e-5 seconds
From worker 5: [ Info: 2022-07-08 23:16:26 : Solving point 5 of 5
From worker 5: [ Info: 2022-07-08 23:16:26 : Solver used: AMG accelerated by CG
From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to construct preconditioner = 3.9709e-5 seconds
From worker 5: [ Info: 2022-07-08 23:16:26 : Time taken to solve linear system = 1.0917e-5 seconds
┌ Warning: 2022-07-08 23:16:27 : Code to include pairs is activated, some entries did not match with focal node file. Some focal nodes may have been dropped
└ @ Circuitscape ~/.julia/packages/Circuitscape/QbA2E/src/logging.jl:25
Test Summary: | Pass Error Total
Double Precision Tests | 383 2 385
Network Pairwise | 141 141
Network Advanced | 12 12
Raster Pairwise | 1 1
Raster Advanced | 1 1
Raster One to All | 134 134
Raster All to One | 96 96
ERROR: LoadError: Some tests did not pass: 383 passed, 0 failed, 2 errored, 0 broken.
in expression starting at /Users/tjd66/.julia/packages/Circuitscape/QbA2E/test/runtests.jl:15

ViralBShah commented

@ranjanan Using this issue to discuss the Pkg test failures. It doesn't appear to be an issue with Circuitscape based on the issue Simon links to above.

  • 👍1
ruegdeg commented

Dear all, I tried to make the Julia Circuitscape to work within a Singularity container, but always getting this error about SimpleWeightedGraphs:
LoadError: MethodError: no method matching connected_components(::SimpleWeightedGraphs.SimpleWeightedGraph{Int32,Float64})
Closest candidates are:
connected_components(!Matched::LightGraphs.AbstractGraph{T}) where T at /home/XX/.julia/packages/LightGraphs/IgJif/src/connectivity.jl:101
..
.
.
Any suggestions how to overcome this?

ViralBShah commented

I can't imagine the Singularity container is different from running it regularly. Not sure what is causing this.

ViralBShah commented

I'm closing this since it is quite old now. Please reopen a new issue if tests still failing. I just ran everything with Julia 1.10 and works fine.