Package: actimetrics
Check: R code for possible problems
New result: NOTE
  acti_calculate_measures: no visible global function definition for
    ‘flag_qc_all’
  Undefined global functions or variables:
    flag_qc_all

Package: actimetrics
Check: tests
New result: ERROR
    Running ‘testthat.R’ [110s/171s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > if (rlang::is_installed("stepcount") && rlang::is_installed("reticulate")) {
    +   try({
    +     reticulate::py_require("stepcount==3.11.0", python_version = "3.10",
    +                            action = "add")
    +     reticulate::import("stepcount")
    +   })
    + }
    Downloading cpython-3.10.22-linux-x86_64-gnu (download) (28.0MiB)
     Downloaded cpython-3.10.22-linux-x86_64-gnu (download)
    Downloading torch (846.3MiB)
    Downloading nvidia-cublas-cu11 (302.4MiB)
    Downloading pillow (6.6MiB)
    Downloading matplotlib (11.0MiB)
    Downloading nvidia-cuda-nvrtc-cu11 (20.0MiB)
    Downloading nvidia-cudnn-cu11 (531.3MiB)
    Downloading numpy (16.5MiB)
    Downloading scipy (32.8MiB)
    Downloading fonttools (5.0MiB)
    Downloading pandas (11.7MiB)
    Downloading kiwisolver (1.6MiB)
    Downloading statsmodels (11.5MiB)
    Downloading llvmlite (41.6MiB)
    Downloading torchvision (23.1MiB)
    Downloading scikit-learn (29.0MiB)
    Downloading numba (3.5MiB)
     Downloaded kiwisolver
     Downloaded numba
     Downloaded fonttools
     Downloaded pillow
     Downloaded matplotlib
     Downloaded statsmodels
     Downloaded pandas
     Downloaded numpy
     Downloaded nvidia-cuda-nvrtc-cu11
     Downloaded scipy
     Downloaded torchvision
     Downloaded scikit-learn
     Downloaded llvmlite
     Downloaded nvidia-cublas-cu11
     Downloaded nvidia-cudnn-cu11
     Downloaded torch
    Installed 46 packages in 151ms
    Module(stepcount)
    > Sys.setenv(SSQ_PARALLEL = 0)
    > library(testthat)
    > library(actimetrics)
    > 
    > 
    > test_check("actimetrics")
    Saving _problems/test-coverage-drivers-236.R
    ================================================================================
    [1] "Creating Downsampled Data"
    [1] "Filtering Data"
    [1] "Trimming Data"
    [1] "Getting data back to 10Hz for accumulation"
    [1] "Summing epochs"
    [1] "Creating Downsampled Data"
    [1] "Filtering Data"
    [1] "Trimming Data"
    [1] "Getting data back to 10Hz for accumulation"
    [1] "Summing epochs"
    Loading chunk: 1Loading chunk: 1Saving _problems/test-step-walking-91.R
    Saving _problems/test-step-walking-96.R
    Downloading https://wearables-files.ndph.ox.ac.uk/files/models/stepcount/ssl-20230208.joblib.lzma...
    Gravity calibration...
    Gravity calibration... Done! (0.01s)
    Nonwear detection...
    Nonwear detection... Done! (0.03s)
    Resampling...
    Resampling... Done! (0.01s)
    Defining windows...
    
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    100%|██████████| 241/241 [00:00<00:00, 2581.31it/s]
    Downloading: "https://github.com/OxWearables/ssl-wearables/zipball/v1.0.0" to /home/hornik/tmp/scratch/check-CRAN-incoming-hornik/cache/R/reticulate/uv/cache/archive-v0/fvBRbbQe69k-POsI/lib/python3.10/site-packages/stepcount/torch_hub_cache/v1.0.0.zip
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    Saving _problems/test-summary-68.R
    ================================================================================
    [1] "Creating Downsampled Data"
    [1] "Filtering Data"
    [1] "Trimming Data"
    [1] "Getting data back to 10Hz for accumulation"
    [1] "Summing epochs"
    [ FAIL 4 | WARN 7 | SKIP 1 | PASS 106 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • empty test (1): 'test-stepcount.R:1:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-coverage-drivers.R:218:3'): measure wrappers and calibration can be driven by mocks ──
    Error in `testthat::local_mocked_bindings(acti_fill_zeros = function(data) data, flag_qc_all = function(data, dynamic_range, verbose, flags) {     dplyr::mutate(data, flag_low = 1L) }, acti_calculate_counts = function(data, epoch = 60L, resample = TRUE, lfe_select = FALSE, verbose = TRUE) {     tibble::tibble(time = as.POSIXct("2020-01-01 00:00:00", tz = "UTC"), counts = 5) }, acti_calculate_mims = function(data, unit = "1 min", dynamic_range = NULL, ...) {     tibble::tibble(HEADER_TIME_STAMP = as.POSIXct("2020-01-01 00:00:00", tz = "UTC"), MIMS = 7) }, .package = "actimetrics")`: Can't find binding for `flag_qc_all`
    Backtrace:
        ▆
     1. └─testthat::local_mocked_bindings(...) at test-coverage-drivers.R:218:3
     2.   └─cli::cli_abort("Can't find binding for {.arg {missing}}")
     3.     └─rlang::abort(...)
    ── Failure ('test-step-walking.R:89:3'): stepcount and sdt infer sample rate when missing ──
    Expected `{ ... }` to produce warnings.
    ── Failure ('test-step-walking.R:94:3'): stepcount and sdt infer sample rate when missing ──
    Expected `{ ... }` to produce warnings.
    ── Error ('test-summary.R:60:3'): calculate_measures combines summary outputs ──
    <functionNotFoundError/objectNotFoundError/error/condition>
    Error in `flag_qc_all(data, dynamic_range = dynamic_range, verbose = verbose, flags = flags)`: could not find function "flag_qc_all"
    Backtrace:
        ▆
     1. └─actimetrics::acti_calculate_measures(...) at test-summary.R:60:3
    
    [ FAIL 4 | WARN 7 | SKIP 1 | PASS 106 ]
    Error:
    ! Test failures.
    Execution halted