Last updated on 2025-03-10 18:53:14 CET.
| Package | ERROR | OK |
|---|---|---|
| jlme | 5 | 10 |
| jlmerclusterperm | 3 | 12 |
| JuliaFormulae | 15 |
Current CRAN status: ERROR: 5, OK: 10
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [1m/15m]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(jlme)
>
> test_check("jlme")
Starting Julia ...
Connecting to Julia TCP server at localhost:11980 ...
[1] 11980
Julia version 1.11.0 detected.
No active Julia connection. Please call `jlme_setup()`.
[1] FALSE
julia
"/usr/bin/julia"
Starting Julia (v1.11.0) ...
Activating new project at `/tmp/RtmpL3pZA7/working_dir/jl_7TLUYz`
Resolving package versions...
Updating `/tmp/RtmpL3pZA7/working_dir/jl_7TLUYz/Project.toml`
[38e38edf] + GLM v1.9.0
[ff71e718] + MixedModels v4.31.0
[3eaba693] + StatsModels v0.7.4
Updating `/tmp/RtmpL3pZA7/working_dir/jl_7TLUYz/Manifest.toml`
[79e6a3ab] + Adapt v4.2.0
[66dad0bd] + AliasTables v1.1.3
[4c555306] + ArrayLayouts v1.11.1
[69666777] + Arrow v2.8.0
[31f734f8] + ArrowTypes v2.3.0
[093aae92] + BSplineKit v0.18.2
[aae01518] + BandedMatrices v1.9.2
[c3b6d118] + BitIntegers v0.3.2
[fa961155] + CEnum v0.5.0
[5ba52731] + CodecLz4 v0.4.5
[6b39b394] + CodecZstd v0.8.6
[bbf7d656] + CommonSubexpressions v0.3.1
[f70d9fcc] + CommonWorldInvalidations v1.0.0
[34da2185] + Compat v4.16.0
[f0e56b4a] + ConcurrentUtilities v2.5.0
[9a962f9c] + DataAPI v1.16.0
[864edb3b] + DataStructures v0.18.20
[e2d170a0] + DataValueInterfaces v1.0.0
[85a47980] + Dictionaries v0.4.4
[163ba53b] + DiffResults v1.1.0
[b552c78f] + DiffRules v1.15.1
[31c24e10] + Distributions v0.25.117
[ffbed154] + DocStringExtensions v0.9.3
[4e289a0a] + EnumX v1.0.4
[e2ba6199] + ExprTools v0.1.10
[442a2c76] + FastGaussQuadrature v1.0.2
[1a297f60] + FillArrays v1.13.0
[f6369f11] + ForwardDiff v0.10.38
[38e38edf] + GLM v1.9.0
[34004b35] + HypergeometricFunctions v0.3.27
[615f187c] + IfElse v0.1.1
[313cdc1a] + Indexing v1.1.1
[842dd82b] + InlineStrings v1.4.3
[92d709cd] + IrrationalConstants v0.2.4
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.7.0
[0f8b85d8] + JSON3 v1.14.1
[2ab3a3ac] + LogExpFunctions v0.3.29
[1914dd2f] + MacroTools v0.5.15
[e1d29d7a] + Missings v1.2.0
[ff71e718] + MixedModels v4.31.0
[7e9fb7ac] + MixedModelsDatasets v0.1.2
[78c3b35d] + Mocking v0.8.1
[76087f3c] + NLopt v1.1.3
[77ba4419] + NaNMath v1.1.2
[bac558e1] + OrderedCollections v1.8.0
[90014a1f] + PDMats v0.11.32
[69de0a69] + Parsers v2.8.1
[2dfb63ee] + PooledArrays v1.4.3
[aea7be01] + PrecompileTools v1.2.1
[21216c6a] + Preferences v1.4.3
[92933f4c] + ProgressMeter v1.10.2
[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
[6c6a2e73] + Scratch v1.2.1
[91c51154] + SentinelArrays v1.4.8
[1277b4bf] + ShiftedArrays v2.0.0
[a2af1166] + SortingAlgorithms v1.2.1
[276daf66] + SpecialFunctions v2.5.0
[03a91e81] + SplitApplyCombine v1.2.3
[aedffcd0] + Static v1.1.1
[90137ffa] + StaticArrays v1.9.13
[1e83bf80] + StaticArraysCore v1.4.3
[10745b16] + Statistics v1.11.1
[82ae8749] + StatsAPI v1.7.0
[2913bbd2] + StatsBase v0.34.4
[4c63d2b9] + StatsFuns v1.3.2
[3eaba693] + StatsModels v0.7.4
[354b36f9] + StringViews v1.3.4
[856f2bd8] + StructTypes v1.11.0
[dc5dba14] + TZJData v1.4.0+2025a
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.12.0
[f269a46b] + TimeZones v1.21.3
[3bb67fe8] + TranscodingStreams v0.11.3
[9d95f2ec] + TypedTables v1.4.6
[5ced341a] + Lz4_jll v1.10.1+0
[079eb43e] + NLopt_jll v2.10.0+0
[efe28fd5] + OpenSpecFun_jll v0.5.6+0
[f50d1b31] + Rmath_jll v0.5.1+0
[3161d3a3] + Zstd_jll v1.5.7+1
[0dad84c5] + ArgTools v1.1.2
[56f22d72] + Artifacts v1.11.0
[2a0f44e3] + Base64 v1.11.0
[ade2ca70] + Dates v1.11.0
[8ba89e20] + Distributed v1.11.0
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching v1.11.0
[9fa8497b] + Future v1.11.0
[b77e0a4c] + InteractiveUtils v1.11.0
[4af54fe1] + LazyArtifacts v1.11.0
[b27032c2] + LibCURL v0.6.4
[76f85450] + LibGit2 v1.11.0
[8f399da3] + Libdl v1.11.0
[37e2e46d] + LinearAlgebra v1.11.0
[56ddb016] + Logging v1.11.0
[d6f4376e] + Markdown v1.11.0
[a63ad114] + Mmap v1.11.0
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.11.0
[de0858da] + Printf v1.11.0
[3fa0cd96] + REPL v1.11.0
[9a3f8284] + Random v1.11.0
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization v1.11.0
[6462fe0b] + Sockets v1.11.0
[2f01184e] + SparseArrays v1.11.0
[f489334b] + StyledStrings v1.11.0
[4607b0f0] + SuiteSparse
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[cf7118a7] + UUIDs v1.11.0
[4ec0a83e] + Unicode v1.11.0
[e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
[deac9b47] + LibCURL_jll v8.6.0+0
[e37daf67] + LibGit2_jll v1.7.2+0
[29816b5a] + LibSSH2_jll v1.11.0+1
[c8ffd9c3] + MbedTLS_jll v2.28.6+0
[14a3606d] + MozillaCACerts_jll v2023.12.12
[4536629a] + OpenBLAS_jll v0.3.27+1
[05823500] + OpenLibm_jll v0.8.1+2
[bea87d4a] + SuiteSparse_jll v7.7.0+0
[83775a58] + Zlib_jll v1.2.13+1
[8e850b90] + libblastrampoline_jll v5.11.0+0
[8e850ede] + nghttp2_jll v1.59.0+0
[3f19e933] + p7zip_jll v17.4.0+2
Successfully set up Julia connection. (115s)
user system elapsed
0.116 0.082 116.137
jlme 0.4.1
R Under development (unstable) (2025-03-06 r87893)
Julia Version 1.11.0-rc3
Commit 616e45539d (2024-08-26 15:46 UTC)
Build Info:
Fedora 40 build
Note: This is an unofficial build, please report bugs to the project
responsible for this build and not to the Julia project unless you can
reproduce the issue using official builds available at https://julialang.org/downloads
Platform Info:
OS: Linux (x86_64-redhat-linux)
CPU: 24 × Intel(R) Xeon(R) CPU E5-2440 0 @ 2.40GHz
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, sandybridge)
Threads: 1 default, 0 interactive, 1 GC (on 24 virtual cores)
Environment:
LD_LIBRARY_PATH =
Status `/tmp/RtmpL3pZA7/working_dir/jl_7TLUYz/Project.toml`
[38e38edf] GLM v1.9.0
[ff71e718] MixedModels v4.31.0
[3eaba693] StatsModels v0.7.4
[1] TRUE
Julia already running - skipping. Did you mean `restart = TRUE`?
[1] TRUE
┌ Warning: Reverse spline for θ3 is not monotone.
└ @ MixedModels /data/gannet/ripley/.julia/packages/MixedModels/UklDx/src/profile/thetapr.jl:101
Progress: 20%|████████▎ | ETA: 0:00:08
Progress: 100%|█████████████████████████████████████████| Time: 0:00:03
[ FAIL 3 | WARN 8 | SKIP 0 | PASS 50 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-model.R:38:3'): reproduces `lm()` and `lmer()` outputs ───────
`x_res` (`actual`) not identical to `y_res` (`expected`).
`actual`: 300.000 10.000 0.070 20.000 6.000 30.000
`expected`: 300.000 10.000 0.000 20.000 20.000 20.000
Backtrace:
▆
1. └─jlme:::expect_similar_models(jmod2, rmod2) at test-model.R:38:3
2. └─testthat::expect_identical(x_res, y_res) at tests/testthat/helper-equivalence.R:22:3
── Failure ('test-model.R:105:5'): formula conversions work ────────────────────
`x_res` (`actual`) not identical to `y_res` (`expected`).
`actual`: 300.0 10.0 30.0 6.0 30.0
`expected`: 300.0 10.0 20.0 20.0 20.0
Backtrace:
▆
1. └─jlme:::expect_similar_models(j_zcp, r_zcp) at test-model.R:105:5
2. └─testthat::expect_identical(x_res, y_res) at tests/testthat/helper-equivalence.R:22:3
── Failure ('test-model.R:110:5'): formula conversions work ────────────────────
`x_res` (`actual`) not identical to `y_res` (`expected`).
`actual`: -800.0 10.0 40.0 30.0
`expected`: -800.0 10.0 30.0 30.0
Backtrace:
▆
1. └─jlme:::expect_similar_models(j_protect, r_protect, ignore_names = TRUE) at test-model.R:110:5
2. └─testthat::expect_identical(x_res, y_res) at tests/testthat/helper-equivalence.R:22:3
[ FAIL 3 | WARN 8 | SKIP 0 | PASS 50 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [1m/10m]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(jlme)
>
> test_check("jlme")
Starting Julia ...
Connecting to Julia TCP server at localhost:11980 ...
[1] 11980
Julia version 1.11.0 detected.
No active Julia connection. Please call `jlme_setup()`.
[1] FALSE
julia
"/usr/bin/julia"
Starting Julia (v1.11.0) ...
Activating new project at `/tmp/Rtmp6YCm9G/working_dir/jl_D4R17c`
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Updating `/tmp/Rtmp6YCm9G/working_dir/jl_D4R17c/Project.toml`
[38e38edf] + GLM v1.9.0
[ff71e718] + MixedModels v4.31.0
[3eaba693] + StatsModels v0.7.4
Updating `/tmp/Rtmp6YCm9G/working_dir/jl_D4R17c/Manifest.toml`
[79e6a3ab] + Adapt v4.2.0
[66dad0bd] + AliasTables v1.1.3
[4c555306] + ArrayLayouts v1.11.1
[69666777] + Arrow v2.8.0
[31f734f8] + ArrowTypes v2.3.0
[093aae92] + BSplineKit v0.18.2
[aae01518] + BandedMatrices v1.9.2
[c3b6d118] + BitIntegers v0.3.2
[fa961155] + CEnum v0.5.0
[5ba52731] + CodecLz4 v0.4.5
[6b39b394] + CodecZstd v0.8.6
[bbf7d656] + CommonSubexpressions v0.3.1
[f70d9fcc] + CommonWorldInvalidations v1.0.0
[34da2185] + Compat v4.16.0
[f0e56b4a] + ConcurrentUtilities v2.5.0
[9a962f9c] + DataAPI v1.16.0
[864edb3b] + DataStructures v0.18.20
[e2d170a0] + DataValueInterfaces v1.0.0
[85a47980] + Dictionaries v0.4.4
[163ba53b] + DiffResults v1.1.0
[b552c78f] + DiffRules v1.15.1
[31c24e10] + Distributions v0.25.117
[ffbed154] + DocStringExtensions v0.9.3
[4e289a0a] + EnumX v1.0.4
[e2ba6199] + ExprTools v0.1.10
[442a2c76] + FastGaussQuadrature v1.0.2
[1a297f60] + FillArrays v1.13.0
[f6369f11] + ForwardDiff v0.10.38
[38e38edf] + GLM v1.9.0
[34004b35] + HypergeometricFunctions v0.3.27
[615f187c] + IfElse v0.1.1
[313cdc1a] + Indexing v1.1.1
[842dd82b] + InlineStrings v1.4.3
[92d709cd] + IrrationalConstants v0.2.4
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.7.0
[0f8b85d8] + JSON3 v1.14.1
[2ab3a3ac] + LogExpFunctions v0.3.29
[1914dd2f] + MacroTools v0.5.15
[e1d29d7a] + Missings v1.2.0
[ff71e718] + MixedModels v4.31.0
[7e9fb7ac] + MixedModelsDatasets v0.1.2
[78c3b35d] + Mocking v0.8.1
[76087f3c] + NLopt v1.1.3
[77ba4419] + NaNMath v1.1.2
[bac558e1] + OrderedCollections v1.8.0
[90014a1f] + PDMats v0.11.32
[69de0a69] + Parsers v2.8.1
[2dfb63ee] + PooledArrays v1.4.3
[aea7be01] + PrecompileTools v1.2.1
[21216c6a] + Preferences v1.4.3
[92933f4c] + ProgressMeter v1.10.2
[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
[6c6a2e73] + Scratch v1.2.1
[91c51154] + SentinelArrays v1.4.8
[1277b4bf] + ShiftedArrays v2.0.0
[a2af1166] + SortingAlgorithms v1.2.1
[276daf66] + SpecialFunctions v2.5.0
[03a91e81] + SplitApplyCombine v1.2.3
[aedffcd0] + Static v1.1.1
[90137ffa] + StaticArrays v1.9.13
[1e83bf80] + StaticArraysCore v1.4.3
[10745b16] + Statistics v1.11.1
[82ae8749] + StatsAPI v1.7.0
[2913bbd2] + StatsBase v0.34.4
[4c63d2b9] + StatsFuns v1.3.2
[3eaba693] + StatsModels v0.7.4
[354b36f9] + StringViews v1.3.4
[856f2bd8] + StructTypes v1.11.0
[dc5dba14] + TZJData v1.4.0+2025a
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.12.0
[f269a46b] + TimeZones v1.21.3
[3bb67fe8] + TranscodingStreams v0.11.3
[9d95f2ec] + TypedTables v1.4.6
[5ced341a] + Lz4_jll v1.10.1+0
[079eb43e] + NLopt_jll v2.10.0+0
[efe28fd5] + OpenSpecFun_jll v0.5.6+0
[f50d1b31] + Rmath_jll v0.5.1+0
[3161d3a3] + Zstd_jll v1.5.7+1
[0dad84c5] + ArgTools v1.1.2
[56f22d72] + Artifacts v1.11.0
[2a0f44e3] + Base64 v1.11.0
[ade2ca70] + Dates v1.11.0
[8ba89e20] + Distributed v1.11.0
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching v1.11.0
[9fa8497b] + Future v1.11.0
[b77e0a4c] + InteractiveUtils v1.11.0
[4af54fe1] + LazyArtifacts v1.11.0
[b27032c2] + LibCURL v0.6.4
[76f85450] + LibGit2 v1.11.0
[8f399da3] + Libdl v1.11.0
[37e2e46d] + LinearAlgebra v1.11.0
[56ddb016] + Logging v1.11.0
[d6f4376e] + Markdown v1.11.0
[a63ad114] + Mmap v1.11.0
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.11.0
[de0858da] + Printf v1.11.0
[3fa0cd96] + REPL v1.11.0
[9a3f8284] + Random v1.11.0
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization v1.11.0
[6462fe0b] + Sockets v1.11.0
[2f01184e] + SparseArrays v1.11.0
[f489334b] + StyledStrings v1.11.0
[4607b0f0] + SuiteSparse
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[cf7118a7] + UUIDs v1.11.0
[4ec0a83e] + Unicode v1.11.0
[e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
[deac9b47] + LibCURL_jll v8.6.0+0
[e37daf67] + LibGit2_jll v1.7.2+0
[29816b5a] + LibSSH2_jll v1.11.0+1
[c8ffd9c3] + MbedTLS_jll v2.28.6+0
[14a3606d] + MozillaCACerts_jll v2023.12.12
[4536629a] + OpenBLAS_jll v0.3.27+1
[05823500] + OpenLibm_jll v0.8.1+2
[bea87d4a] + SuiteSparse_jll v7.7.0+0
[83775a58] + Zlib_jll v1.2.13+1
[8e850b90] + libblastrampoline_jll v5.11.0+0
[8e850ede] + nghttp2_jll v1.59.0+0
[3f19e933] + p7zip_jll v17.4.0+2
Successfully set up Julia connection. (74s)
user system elapsed
0.104 0.068 74.821
jlme 0.4.1
R Under development (unstable) (2025-03-07 r87895)
Julia Version 1.11.0-rc3
Commit 616e45539d (2024-08-26 15:46 UTC)
Build Info:
Fedora 40 build
Note: This is an unofficial build, please report bugs to the project
responsible for this build and not to the Julia project unless you can
reproduce the issue using official builds available at https://julialang.org/downloads
Platform Info:
OS: Linux (x86_64-redhat-linux)
CPU: 24 × Intel(R) Xeon(R) CPU E5-2440 0 @ 2.40GHz
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, sandybridge)
Threads: 1 default, 0 interactive, 1 GC (on 24 virtual cores)
Environment:
LD_LIBRARY_PATH =
Status `/tmp/Rtmp6YCm9G/working_dir/jl_D4R17c/Project.toml`
[38e38edf] GLM v1.9.0
[ff71e718] MixedModels v4.31.0
[3eaba693] StatsModels v0.7.4
[1] TRUE
Julia already running - skipping. Did you mean `restart = TRUE`?
[1] TRUE
┌ Warning: Reverse spline for θ3 is not monotone.
└ @ MixedModels /data/gannet/ripley/.julia/packages/MixedModels/UklDx/src/profile/thetapr.jl:101
Progress: 20%|████████▎ | ETA: 0:00:11
Progress: 100%|█████████████████████████████████████████| Time: 0:00:04
[ FAIL 3 | WARN 8 | SKIP 0 | PASS 50 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-model.R:38:3'): reproduces `lm()` and `lmer()` outputs ───────
`x_res` (`actual`) not identical to `y_res` (`expected`).
`actual`: 300.000 10.000 0.070 20.000 6.000 30.000
`expected`: 300.000 10.000 0.000 20.000 20.000 20.000
Backtrace:
▆
1. └─jlme:::expect_similar_models(jmod2, rmod2) at test-model.R:38:3
2. └─testthat::expect_identical(x_res, y_res) at tests/testthat/helper-equivalence.R:22:3
── Failure ('test-model.R:105:5'): formula conversions work ────────────────────
`x_res` (`actual`) not identical to `y_res` (`expected`).
`actual`: 300.0 10.0 30.0 6.0 30.0
`expected`: 300.0 10.0 20.0 20.0 20.0
Backtrace:
▆
1. └─jlme:::expect_similar_models(j_zcp, r_zcp) at test-model.R:105:5
2. └─testthat::expect_identical(x_res, y_res) at tests/testthat/helper-equivalence.R:22:3
── Failure ('test-model.R:110:5'): formula conversions work ────────────────────
`x_res` (`actual`) not identical to `y_res` (`expected`).
`actual`: -800.0 10.0 40.0 30.0
`expected`: -800.0 10.0 30.0 30.0
Backtrace:
▆
1. └─jlme:::expect_similar_models(j_protect, r_protect, ignore_names = TRUE) at test-model.R:110:5
2. └─testthat::expect_identical(x_res, y_res) at tests/testthat/helper-equivalence.R:22:3
[ FAIL 3 | WARN 8 | SKIP 0 | PASS 50 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running 'testthat.R' [43s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(jlme)
>
> test_check("jlme")
Starting Julia ...
Connecting to Julia TCP server at localhost:11980 ...
[1] 11980
Julia version 1.11.3 detected.
No active Julia connection. Please call `jlme_setup()`.
[1] FALSE
julia
"C:\\PROGRA~1\\Julia\\bin\\julia.exe"
Starting Julia (v1.11.3) ...
Activating new project at `D:\temp\2025_03_07_01_50_00_19112\jl_sVHTQB`
Updating registry at `C:\Users\CRAN\.julia\registries\General.toml`
Resolving package versions...
Timing stopped at: 0.03 0.05 19.53
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-model.R:11:3'): (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] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
@ Pkg.Operations C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1467
[9] add
@ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1414 [inlined]
[10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:312
[11] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:159
[12] add(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:148
[13] add(pkgs::Vector{String})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:147
[14] top-level scope
@ string:4
[15] eval
@ .\boot.jl:430 [inlined]
[16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
@ Base .\loading.jl:2734
[17] include_string (repeats 2 times)
@ .\loading.jl:2744 [inlined]
[18] mainevalcmd(str::String)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\evaluating.jl:150
[19] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
@ Base .\essentials.jl:1055
[20] invokelatest(::Any, ::Any, ::Vararg{Any})
@ Base .\essentials.jl:1052
[21] evaluate!
@ D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
[22] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket})
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\evaluating.jl:55
[23] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\communicating.jl:185
[24] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\communicating.jl:145
in expression starting at string:4
Backtrace:
▆
1. ├─base::print(...) at test-model.R:10:1
2. ├─base::system.time(...)
3. └─jlme::jlme_setup(restart = TRUE, verbose = TRUE) at test-model.R:11:3
4. ├─base::do.call(.jlme_setup, params)
5. └─jlme (local) `<fn>`(add = NULL, threads = NULL, verbose = TRUE)
6. └─jlme:::init_proj(add = add, verbose = verbose)
7. └─jlme::jl(...)
8. └─JuliaConnectoR::juliaEval(s_interpolated)
9. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
10. ├─base::tryCatch(...)
11. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. └─JuliaConnectoR:::doCallJulia(funName, jlargs)
15. └─JuliaConnectoR:::handleCallbacksAndOutput()
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.4.1
Check: tests
Result: ERROR
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(jlme)
>
> test_check("jlme")
Starting Julia ...
Connecting to Julia TCP server at localhost:11980 ...
[1] 11980
Julia version 1.11.3 detected.
No active Julia connection. Please call `jlme_setup()`.
[1] FALSE
julia
"C:\\PROGRA~1\\Julia\\bin\\julia.exe"
Starting Julia (v1.11.3) ...
Activating new project at `D:\temp\2025_03_09_01_50_00_26348\jl_M9TD3K`
Updating registry at `C:\Users\CRAN\.julia\registries\General.toml`
Resolving package versions...
Timing stopped at: 0.02 0.05 18.6
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-model.R:11:3'): (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] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
@ Pkg.Operations C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1467
[9] add
@ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1414 [inlined]
[10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:312
[11] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:159
[12] add(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:148
[13] add(pkgs::Vector{String})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:147
[14] top-level scope
@ string:4
[15] eval
@ .\boot.jl:430 [inlined]
[16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
@ Base .\loading.jl:2734
[17] include_string (repeats 2 times)
@ .\loading.jl:2744 [inlined]
[18] mainevalcmd(str::String)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:150
[19] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
@ Base .\essentials.jl:1055
[20] invokelatest(::Any, ::Any, ::Vararg{Any})
@ Base .\essentials.jl:1052
[21] evaluate!
@ D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
[22] 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
[23] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:185
[24] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.4\JuliaConnectoR\Julia\communicating.jl:145
in expression starting at string:4
Backtrace:
▆
1. ├─base::print(...) at test-model.R:10:1
2. ├─base::system.time(...)
3. └─jlme::jlme_setup(restart = TRUE, verbose = TRUE) at test-model.R:11:3
4. ├─base::do.call(.jlme_setup, params)
5. └─jlme (local) `<fn>`(add = NULL, threads = NULL, verbose = TRUE)
6. └─jlme:::init_proj(add = add, verbose = verbose)
7. └─jlme::jl(...)
8. └─JuliaConnectoR::juliaEval(s_interpolated)
9. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
10. ├─base::tryCatch(...)
11. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. └─JuliaConnectoR:::doCallJulia(funName, jlargs)
15. └─JuliaConnectoR:::handleCallbacksAndOutput()
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.4.1
Check: tests
Result: ERROR
Running 'testthat.R' [36s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(jlme)
>
> test_check("jlme")
Starting Julia ...
Connecting to Julia TCP server at localhost:11980 ...
[1] 11980
Julia version 1.11.3 detected.
No active Julia connection. Please call `jlme_setup()`.
[1] FALSE
julia
"C:\\PROGRA~1\\Julia\\bin\\julia.exe"
Starting Julia (v1.11.3) ...
Activating new project at `D:\temp\2025_03_07_01_50_00_19112\jl_7tIEUh`
Updating registry at `C:\Users\CRAN\.julia\registries\General.toml`
Timing stopped at: 0.02 0.03 18.72
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-model.R:11:3'): (code run outside of `test_that()`) ────────────
Error: Evaluation in Julia failed.
Original Julia error message:
LoadError: IOError: unlink("C:\\Users\\CRAN\\.julia\\registries\\General.tar.gz"): resource busy or locked (EBUSY)
Stacktrace:
[1] uv_error
@ .\libuv.jl:106 [inlined]
[2] unlink(p::String)
@ Base.Filesystem .\file.jl:1105
[3] rm(path::String; force::Bool, recursive::Bool)
@ Base.Filesystem .\file.jl:283
[4] rm
@ .\file.jl:273 [inlined]
[5] checkfor_mv_cp_cptree(src::String, dst::String, txt::String; force::Bool)
@ Base.Filesystem .\file.jl:332
[6] checkfor_mv_cp_cptree
@ .\file.jl:318 [inlined]
[7] #mv#15
@ .\file.jl:427 [inlined]
[8] mv
@ .\file.jl:426 [inlined]
[9] (::Pkg.Registry.var"#75#80"{IOContext{IO}, Dates.Day, Dict{String, Any}, String, Vector{Pkg.Registry.RegistryInstance}})()
@ Pkg.Registry C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Registry\Registry.jl:442
[10] mkpidlock(f::Pkg.Registry.var"#75#80"{IOContext{IO}, Dates.Day, Dict{String, Any}, String, Vector{Pkg.Registry.RegistryInstance}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64})
@ FileWatching.Pidfile C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:95
[11] mkpidlock
@ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:90 [inlined]
[12] update(regs::Vector{Pkg.Registry.RegistrySpec}; io::IOContext{IO}, force::Bool, depots::Vector{String}, update_cooldown::Dates.Day)
@ Pkg.Registry C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Registry\Registry.jl:398
[13] update
@ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Registry\Registry.jl:391 [inlined]
[14] #update#73
@ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Registry\Registry.jl:386 [inlined]
[15] update_registries(ctx::Pkg.Types.Context; force::Bool, kwargs::@Kwargs{update_cooldown::Dates.Day})
@ Pkg.Operations C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1307
[16] update_registries
@ C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\Operations.jl:1304 [inlined]
[17] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:295
[18] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:159
[19] add(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:148
[20] add(pkgs::Vector{String})
@ Pkg.API C:\PROGRA~1\Julia\share\julia\stdlib\v1.11\Pkg\src\API.jl:147
[21] top-level scope
@ string:4
[22] eval
@ .\boot.jl:430 [inlined]
[23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
@ Base .\loading.jl:2734
[24] include_string (repeats 2 times)
@ .\loading.jl:2744 [inlined]
[25] mainevalcmd(str::String)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:150
[26] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
@ Base .\essentials.jl:1055
[27] invokelatest(::Any, ::Any, ::Vararg{Any})
@ Base .\essentials.jl:1052
[28] evaluate!
@ D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:67 [inlined]
[29] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket})
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\evaluating.jl:55
[30] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185
[31] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:145
in expression starting at string:4
Backtrace:
▆
1. ├─base::print(...) at test-model.R:10:1
2. ├─base::system.time(...)
3. └─jlme::jlme_setup(restart = TRUE, verbose = TRUE) at test-model.R:11:3
4. ├─base::do.call(.jlme_setup, params)
5. └─jlme (local) `<fn>`(add = NULL, threads = NULL, verbose = TRUE)
6. └─jlme:::init_proj(add = add, verbose = verbose)
7. └─jlme::jl(...)
8. └─JuliaConnectoR::juliaEval(s_interpolated)
9. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
10. ├─base::tryCatch(...)
11. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. └─JuliaConnectoR:::doCallJulia(funName, jlargs)
15. └─JuliaConnectoR:::handleCallbacksAndOutput()
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 3, OK: 12
Version: 1.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [44s]
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 [9.3s]
i Starting Julia with 2 threads
v Starting Julia with 2 threads [7.7s]
i Activating package environment
x Activating package environment [2.3s]
[ 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\4.5\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\4.5\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\4.5\JuliaConnectoR\Julia\evaluating.jl:55
[24] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\communicating.jl:185
[25] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\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\4.5\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\4.5\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\4.5\JuliaConnectoR\Julia\evaluating.jl:55
[19] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\communicating.jl:185
[20] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\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\4.5\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\4.5\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\4.5\JuliaConnectoR\Julia\evaluating.jl:55
[10] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\communicating.jl:185
[11] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\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\4.5\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\4.5\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\4.5\JuliaConnectoR\Julia\evaluating.jl:55
[19] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\JuliaConnectoR\Julia\communicating.jl:185
[20] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.5\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
Flavor: r-devel-windows-x86_64
Version: 1.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [44s]
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 [7.5s]
ℹ Activating package environment
✖ Activating package environment [8.8s]
i Starting Julia with 2 threads
v Starting Julia with 2 threads [8.1s]
i Activating package environment
x Activating package environment [2.3s]
[ 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
Flavor: r-release-windows-x86_64
Version: 1.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [56s]
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: 56 × Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, broadwell)
Threads: 1 default, 0 interactive, 1 GC (on 56 virtual cores)
nothing
ℹ Starting Julia with 2 threads
✔ Starting Julia with 2 threads [9.9s]
ℹ Activating package environment
✖ Activating package environment [11.1s]
i Starting Julia with 2 threads
v Starting Julia with 2 threads [9.6s]
i Activating package environment
x Activating package environment [2.8s]
[ 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\4.3\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\4.3\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\4.3\JuliaConnectoR\Julia\evaluating.jl:55
[24] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185
[25] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\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\4.3\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\4.3\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\4.3\JuliaConnectoR\Julia\evaluating.jl:55
[19] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185
[20] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\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\4.3\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\4.3\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\4.3\JuliaConnectoR\Julia\evaluating.jl:55
[10] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185
[11] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\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\4.3\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\4.3\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\4.3\JuliaConnectoR\Julia\evaluating.jl:55
[19] serve_repl(sock::Sockets.TCPSocket)
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\JuliaConnectoR\Julia\communicating.jl:185
[20] (::Main.RConnector.var"#3#5")()
@ Main.RConnector D:\RCompile\CRANpkg\lib\4.3\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
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 15