• using R Under development (unstable) (2025-02-15 r87723)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘jlme/DESCRIPTION’ ... OK
• this is package ‘jlme’ version ‘0.4.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘jlme’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [1m/16m] ERROR   Running ‘testthat.R’ [1m/16m] 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/RtmpXmpHoS/working_dir/jl_yDzULb`       Updating registry at `~/.julia/registries/General.toml`      Resolving package versions...      Installed ProgressMeter ─ v1.10.2      Installed GLM ─────────── v1.9.0      Installed StatsBase ───── v0.34.4       Updating `/tmp/RtmpXmpHoS/working_dir/jl_yDzULb/Project.toml`     [38e38edf] + GLM v1.9.0     [ff71e718] + MixedModels v4.30.1     [3eaba693] + StatsModels v0.7.4       Updating `/tmp/RtmpXmpHoS/working_dir/jl_yDzULb/Manifest.toml`     [79e6a3ab] + Adapt v4.1.1     [66dad0bd] + AliasTables v1.1.3     [4c555306] + ArrayLayouts v1.11.0     [69666777] + Arrow v2.8.0     [31f734f8] + ArrowTypes v2.3.0     [093aae92] + BSplineKit v0.18.1     [aae01518] + BandedMatrices v1.9.1     [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 v1.4.2     [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 v4.30.1     [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 v1.3.0     [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 v1.9.12     [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 v1.21.2     [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+0     [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   Precompiling project...      2886.0 ms ✓ IfElse      2901.6 ms ✓ CommonWorldInvalidations      2890.4 ms ✓ PtrArrays      3179.6 ms ✓ Indexing      3418.9 ms ✓ EnumX      3683.0 ms ✓ ExprTools      4284.4 ms ✓ Reexport      4231.8 ms ✓ CEnum      4433.7 ms ✓ ArrowTypes      5317.0 ms ✓ StringViews      5168.5 ms ✓ BitIntegers      5918.2 ms ✓ FillArrays      5963.7 ms ✓ ConcurrentUtilities      3325.1 ms ✓ StaticArraysCore      3320.8 ms ✓ TranscodingStreams      3506.6 ms ✓ TZJData      3792.7 ms ✓ ShiftedArrays      3368.8 ms ✓ Requires      7125.1 ms ✓ ProgressMeter      7211.7 ms ✓ IrrationalConstants      4446.1 ms ✓ NaNMath      4169.1 ms ✓ Scratch      4395.1 ms ✓ SuiteSparse      4480.4 ms ✓ JLLWrappers      2715.6 ms ✓ FillArrays → FillArraysStatisticsExt      3876.3 ms ✓ AliasTables      3303.0 ms ✓ InlineStrings → ArrowTypesExt      4363.3 ms ✓ Mocking      6529.8 ms ✓ StructTypes      4160.7 ms ✓ FillArrays → FillArraysSparseArraysExt      4225.1 ms ✓ DiffResults      3349.4 ms ✓ Adapt      6119.6 ms ✓ Static      6820.0 ms ✓ Dictionaries      4462.4 ms ✓ LogExpFunctions      3079.9 ms ✓ OpenSpecFun_jll      4223.0 ms ✓ Rmath_jll      8171.1 ms ✓ QuadGK     14157.8 ms ✓ MacroTools      4441.3 ms ✓ NLopt_jll     10445.1 ms ✓ SentinelArrays      4687.8 ms ✓ Zstd_jll      4809.4 ms ✓ Lz4_jll      6010.1 ms ✓ PDMats      2847.4 ms ✓ CommonSubexpressions      4269.7 ms ✓ SplitApplyCombine      3137.8 ms ✓ FillArrays → FillArraysPDMatsExt      4868.6 ms ✓ Rmath      4591.3 ms ✓ CodecLz4      5550.0 ms ✓ CodecZstd      6577.4 ms ✓ NLopt     11192.0 ms ✓ StatsBase     12412.1 ms ✓ SpecialFunctions      2988.0 ms ✓ DiffRules      6347.2 ms ✓ HypergeometricFunctions     25997.5 ms ✓ TimeZones      7611.3 ms ✓ StatsFuns     40406.9 ms ✓ StaticArrays     20078.4 ms ✓ ForwardDiff     38500.6 ms ✓ JSON3      2746.5 ms ✓ Adapt → AdaptStaticArraysExt     10983.7 ms ✓ StatsModels      3848.5 ms ✓ StaticArrays → StaticArraysStatisticsExt      2598.1 ms ✓ JSON3 → JSON3ArrowExt      3946.4 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt      4006.9 ms ✓ TypedTables      6578.2 ms ✓ FastGaussQuadrature     20926.3 ms ✓ Distributions     25882.0 ms ✓ Arrow      4121.5 ms ✓ MixedModelsDatasets      7640.8 ms ✓ GLM     56292.0 ms ✓ ArrayLayouts      2543.4 ms ✓ ArrayLayouts → ArrayLayoutsSparseArraysExt     54224.4 ms ✓ BandedMatrices      6895.6 ms ✓ BandedMatrices → BandedMatricesSparseArraysExt     40675.9 ms ✓ BSplineKit    191707.3 ms ✓ MixedModels     77 dependencies successfully precompiled in 375 seconds. 57 already precompiled.     1 dependency had output during precompilation:   ┌ MixedModels   │ Downloading artifact: TestData   └   Successfully set up Julia connection. (431s)      user system elapsed     0.126 0.084 431.727   jlme 0.4.1   R Under development (unstable) (2025-02-15 r87723)   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/RtmpXmpHoS/working_dir/jl_yDzULb/Project.toml`     [38e38edf] GLM v1.9.0     [ff71e718] MixedModels v4.30.1     [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/FmwXQ/src/profile/thetapr.jl:101      Progress: 20%|████████▎ | ETA: 0:00:07   Progress: 100%|█████████████████████████████████████████| Time: 0:00:02   [ 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
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR