Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(jlmerclusterperm)
  > 
  > test_check("jlmerclusterperm")
  Julia Version 1.11.3
  Commit d63adeda50 (2025-01-21 19:42 UTC)
  Build Info:
    Official https://julialang.org/ release
  Platform Info:
    OS: Windows (x86_64-w64-mingw32)
    CPU: 48 × AMD EPYC 7443 24-Core Processor                
    WORD_SIZE: 64
    LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
  Threads: 1 default, 0 interactive, 1 GC (on 96 virtual cores)
  nothing
  ℹ Starting Julia with 2 threads
  ✔ Starting Julia with 2 threads [7.7s]
  
  ℹ Activating package environment
  ✖ Activating package environment [9s]
  
  i Starting Julia with 2 threads
  v Starting Julia with 2 threads [7.6s]
  
  i Activating package environment
  x Activating package environment [2.4s]
  
  [ FAIL 5 | WARN 0 | SKIP 7 | PASS 5 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-jlmer.R:1:1', 'test-julia_rng.R:1:1',
    'test-permute.R:1:1', 'test-progress.R:1:1', 'test-singularity.R:1:1',
    'test-threshold_search.R:1:1', 'test-timewise_statistics.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-aaa-a-logging.R:7:1'): (code run outside of `test_that()`) ─────
  Error: Evaluation in Julia failed.
  Original Julia error message:
  LoadError: `Distributions=31c24e10-a181-5473-b8eb-7969acd0382f` depends on `Test=8dfed614-e22c-5e08-85e1-65c5234f0b40`, but no such entry exists in the manifest.
  Stacktrace:
    [1] pkgerror(::String, ::Vararg{String})
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:68
    [2] validate_manifest(julia_version::VersionNumber, manifest_format::VersionNumber, stage1::Dict{String, Vector{Pkg.Types.Stage1}}, other::Dict{String, Any})
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:135
    [3] Pkg.Types.Manifest(raw::Dict{String, Any}, f_or_io::String)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:203
    [4] read_manifest(f_or_io::String)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:226
    [5] Pkg.Types.EnvCache(env::Nothing)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:373
    [6] EnvCache
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:351 [inlined]
    [7] #show_update#170
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:2549 [inlined]
    [8] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
      @ Pkg.Operations C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1495
    [9] develop
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1480 [inlined]
   [10] develop(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; shared::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::@Kwargs{io::Base.DevNull})
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:258
   [11] develop(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.DevNull, kwargs::@Kwargs{})
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:159
   [12] develop
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:148 [inlined]
   [13] develop
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:146 [inlined]
   [14] develop(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::String, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::@Kwargs{io::Base.DevNull})
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:176
   [15] top-level scope
      @ string:1
   [16] eval
      @ .\boot.jl:430 [inlined]
   [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base .\loading.jl:2734
   [18] include_string (repeats 2 times)
      @ .\loading.jl:2744 [inlined]
   [19] mainevalcmd(str::String)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:150
   [20] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
      @ Base .\essentials.jl:1055
   [21] invokelatest(::Any, ::Any, ::Vararg{Any})
      @ Base .\essentials.jl:1052
   [22] evaluate!
      @ D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
   [23] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket})
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:55
   [24] serve_repl(sock::Sockets.TCPSocket)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:185
   [25] (::Main.RConnector.var"#3#5")()
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:145
  in expression starting at string:1
  Backtrace:
      ▆
   1. └─jlmerclusterperm:::set_projenv(cache_dir = tempdir(), verbose = TRUE) at test-aaa-a-logging.R:7:1
   2.   └─JuliaConnectoR::juliaEval("Pkg.develop(path = \"JlmerClusterPerm\", io = devnull)")
   3.     └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
   4.       ├─base::tryCatch(...)
   5.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   8.       └─JuliaConnectoR:::doCallJulia(funName, jlargs)
   9.         └─JuliaConnectoR:::handleCallbacksAndOutput()
  ── Error ('test-aaa-b-setup.R:7:3'): Setup with seed works (use 2 for testing) ──
  Error: Evaluation in Julia failed.
  Original Julia error message:
  LoadError: `Distributions=31c24e10-a181-5473-b8eb-7969acd0382f` depends on `Test=8dfed614-e22c-5e08-85e1-65c5234f0b40`, but no such entry exists in the manifest.
  Stacktrace:
    [1] pkgerror(::String, ::Vararg{String})
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:68
    [2] validate_manifest(julia_version::VersionNumber, manifest_format::VersionNumber, stage1::Dict{String, Vector{Pkg.Types.Stage1}}, other::Dict{String, Any})
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:135
    [3] Pkg.Types.Manifest(raw::Dict{String, Any}, f_or_io::String)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:203
    [4] read_manifest(f_or_io::String)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:226
    [5] Pkg.Types.EnvCache(env::Nothing)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:373
    [6] EnvCache
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:351 [inlined]
    [7] add_snapshot_to_undo(env::Nothing)
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:1496
    [8] add_snapshot_to_undo
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:1492 [inlined]
    [9] activate(path::String; shared::Bool, temp::Bool, io::Base.DevNull)
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:1372
   [10] top-level scope
      @ string:1
   [11] eval
      @ .\boot.jl:430 [inlined]
   [12] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base .\loading.jl:2734
   [13] include_string (repeats 2 times)
      @ .\loading.jl:2744 [inlined]
   [14] mainevalcmd(str::String)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:150
   [15] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
      @ Base .\essentials.jl:1055
   [16] invokelatest(::Any, ::Any, ::Vararg{Any})
      @ Base .\essentials.jl:1052
   [17] evaluate!
      @ D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
   [18] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket})
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:55
   [19] serve_repl(sock::Sockets.TCPSocket)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:185
   [20] (::Main.RConnector.var"#3#5")()
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:145
  in expression starting at string:1
  Backtrace:
       ▆
    1. ├─testthat::expect_true(...) at test-aaa-b-setup.R:7:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─jlmerclusterperm::jlmerclusterperm_setup(...)
    5.   └─jlmerclusterperm:::setup_with_progress(...)
    6.     └─jlmerclusterperm:::set_projenv(cache_dir = cache_dir, verbose = verbose)
    7.       └─JuliaConnectoR::juliaEval("Pkg.activate(\".\", io = devnull)")
    8.         └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
    9.           ├─base::tryCatch(...)
   10.           │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.           │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.           │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   13.           └─JuliaConnectoR:::doCallJulia(funName, jlargs)
   14.             └─JuliaConnectoR:::handleCallbacksAndOutput()
  ── Failure ('test-aaa-b-setup.R:13:3'): RNG initializes to seed=1 counter=0 ────
  get_rng_seed() (`actual`) not equal to 1 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (1)
  ── Error ('test-aaa-b-setup.R:14:3'): RNG initializes to seed=1 counter=0 ──────
  Error: Evaluation in Julia failed.
  Original Julia error message:
  LoadError: UndefVarError: `rng` not defined in `Main`
  Suggestion: check for spelling errors or missing imports.
  Stacktrace:
    [1] top-level scope
      @ string:1
    [2] eval
      @ .\boot.jl:430 [inlined]
    [3] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base .\loading.jl:2734
    [4] include_string (repeats 2 times)
      @ .\loading.jl:2744 [inlined]
    [5] mainevalcmd(str::String)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:150
    [6] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
      @ Base .\essentials.jl:1055
    [7] invokelatest(::Any, ::Any, ::Vararg{Any})
      @ Base .\essentials.jl:1052
    [8] evaluate!
      @ D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
    [9] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket})
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:55
   [10] serve_repl(sock::Sockets.TCPSocket)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:185
   [11] (::Main.RConnector.var"#3#5")()
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:145
  in expression starting at string:1
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(get_rng_state(), 0) at test-aaa-b-setup.R:14:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─jlmerclusterperm::get_rng_state()
    5.   └─JuliaConnectoR::juliaEval("Int(rng.ctr1)")
    6.     └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
    7.       ├─base::tryCatch(...)
    8.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11.       └─JuliaConnectoR:::doCallJulia(funName, jlargs)
   12.         └─JuliaConnectoR:::handleCallbacksAndOutput()
  ── Error ('test-clusterpermute.R:3:1'): (code run outside of `test_that()`) ────
  Error: Evaluation in Julia failed.
  Original Julia error message:
  LoadError: `Distributions=31c24e10-a181-5473-b8eb-7969acd0382f` depends on `Test=8dfed614-e22c-5e08-85e1-65c5234f0b40`, but no such entry exists in the manifest.
  Stacktrace:
    [1] pkgerror(::String, ::Vararg{String})
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:68
    [2] validate_manifest(julia_version::VersionNumber, manifest_format::VersionNumber, stage1::Dict{String, Vector{Pkg.Types.Stage1}}, other::Dict{String, Any})
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:135
    [3] Pkg.Types.Manifest(raw::Dict{String, Any}, f_or_io::String)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:203
    [4] read_manifest(f_or_io::String)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\manifest.jl:226
    [5] Pkg.Types.EnvCache(env::Nothing)
      @ Pkg.Types C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:373
    [6] EnvCache
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Types.jl:351 [inlined]
    [7] add_snapshot_to_undo(env::Nothing)
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:1496
    [8] add_snapshot_to_undo
      @ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:1492 [inlined]
    [9] activate(path::String; shared::Bool, temp::Bool, io::Base.DevNull)
      @ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:1372
   [10] top-level scope
      @ string:1
   [11] eval
      @ .\boot.jl:430 [inlined]
   [12] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base .\loading.jl:2734
   [13] include_string (repeats 2 times)
      @ .\loading.jl:2744 [inlined]
   [14] mainevalcmd(str::String)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:150
   [15] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
      @ Base .\essentials.jl:1055
   [16] invokelatest(::Any, ::Any, ::Vararg{Any})
      @ Base .\essentials.jl:1052
   [17] evaluate!
      @ D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
   [18] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket})
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:55
   [19] serve_repl(sock::Sockets.TCPSocket)
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:185
   [20] (::Main.RConnector.var"#3#5")()
      @ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:145
  in expression starting at string:1
  Backtrace:
       ▆
    1. └─jlmerclusterperm::jlmerclusterperm_setup(...) at test-clusterpermute.R:3:1
    2.   └─jlmerclusterperm:::setup_with_progress(...)
    3.     └─jlmerclusterperm:::set_projenv(cache_dir = cache_dir, verbose = verbose)
    4.       └─JuliaConnectoR::juliaEval("Pkg.activate(\".\", io = devnull)")
    5.         └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
    6.           ├─base::tryCatch(...)
    7.           │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    8.           │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9.           │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   10.           └─JuliaConnectoR:::doCallJulia(funName, jlargs)
   11.             └─JuliaConnectoR:::handleCallbacksAndOutput()
  
  [ FAIL 5 | WARN 0 | SKIP 7 | PASS 5 ]
  Error: Test failures
  Execution halted