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Type 'q()' to quit R. > 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") + }) + } Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'stepcount' Run `reticulate::py_last_error()` for details. In addition: Warning message: Some Python package requirements declared via `py_require()` are not installed in the selected Python environment: (C:/Users/CRAN/Documents/.virtualenvs/r-reticulate/Scripts/python.exe) stepcount==3.11.0 > Sys.setenv(SSQ_PARALLEL = 0) > library(testthat) > library(actimetrics) > > > test_check("actimetrics") Saving _problems/test-counts-6.R Running floor_sec on time Summarizing the variance Calculating AI Summarizing the variance Calculating r, ENMO, and flooring time Calculating all MAD measures Calculating r, ENMO, and flooring time Summarizing the variance Calculating all MAD measures Calculating r, ENMO, and flooring time Calculating all MAD measures Calculating r, ENMO, and flooring time Calculating all MAD measures Absolute values Calculting trapezoids Replacing first value as NA Calculating AUCs Absolute values Calculting trapezoids Replacing first value as NA Calculating AUCs Truncating Small AUCs Saving _problems/test-coverage-drivers-244.R Running extrapolation Running filtering Running extrapolation Running filtering Running interpolation Running extrapolation Running filtering Absolute values Calculting trapezoids Replacing first value as NA Calculating AUCs Truncating Small AUCs ================================================================================ Saving _problems/test-regressions-41.R Saving _problems/test-regressions-68.R Saving _problems/test-regressions-87.R Saving _problems/test-regressions-174.R Saving _problems/test-regressions-196.R Saving _problems/test-regressions-232.R Running floor_sec on time Summarizing the variance Calculating AI Running floor_sec on time Summarizing the variance Calculating AI Running floor_sec on time Summarizing the variance Calculating AI Saving _problems/test-regressions-414.R Saving _problems/test-regressions-431.R Saving _problems/test-step-walking-35.R Saving _problems/test-step-walking-90.R Saving _problems/test-step-walking-113.R Saving _problems/test-step-walking-158.R Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'stepcount' Run `reticulate::py_last_error()` for details. Running floor_sec on time Summarizing the variance Calculating AI Running floor_sec on time Summarizing the variance Calculating AI Running floor_sec on time Summarizing the variance Calculating AI Summarizing the variance Calculating r, ENMO, and flooring time Calculating all MAD measures Calculating r, ENMO, and flooring time Calculating all MAD measures Calculating r, ENMO, and flooring time Calculating all MAD measures Absolute values Calculting trapezoids Replacing first value as NA Calculating AUCs Truncating Small AUCs ================================================================================ ================================================================================ ================================================================================ ================================================================================ Calculating r, ENMO, and flooring time Summarizing the variance Calculating all MAD measures ================================================================================ [ FAIL 14 | WARN 4 | SKIP 7 | PASS 153 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • agcounts is not runnable in this session (4): 'test-mims.R:80:5', 'test-mims.R:97:5', 'test-regressions.R:205:5', 'test-wear.R:3:5' • agcounts or MIMSunit is not runnable in this session (1): 'test-summary.R:65:5' • agcounts or actigraph.sleepr is not runnable in this session (1): 'test-mims.R:56:5' • stepcount::stepcount_check() is not TRUE (1): 'test-stepcount.R:10:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-counts.R:4:3'): acti_calculate_counts compares resample strategies ── Error in `acti_standardize_epoch(epoch)`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-counts.R:4:3 2. │ └─base::withCallingHandlers(...) 3. └─actimetrics::acti_calculate_counts(data, resample = TRUE, verbose = FALSE) ── Error ('test-coverage-drivers.R:226:3'): 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:226:3 2. └─cli::cli_abort("Can't find binding for {.arg {missing}}") 3. └─rlang::abort(...) ── Error ('test-regressions.R:41:3'): step summaries keep all-NA epochs as NA, not 0 ── Error in `acti_standardize_epoch(unit, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics:::summarize_to_minute(sdata, prefix = "test") at test-regressions.R:41:3 ── Error ('test-regressions.R:68:3'): acti_calculate_stepcount keeps missing steps and walking as NA ── Error in `acti_standardize_epoch(epoch, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics::acti_calculate_stepcount(data) at test-regressions.R:68:3 ── Error ('test-regressions.R:87:3'): acti_calculate_verisense resolves a single method ── Error in `acti_standardize_epoch(unit, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics::acti_calculate_verisense(data) at test-regressions.R:87:3 2. └─actimetrics:::summarize_to_minute(sdata, prefix = "acti_calculate_verisense") ── Error ('test-regressions.R:170:3'): acti_calculate_counts gives a clear sample rate error ── Error in `acti_standardize_epoch(epoch)`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-regressions.R:170:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─base::suppressWarnings(...) 8. │ └─base::withCallingHandlers(...) 9. └─actimetrics::acti_calculate_counts(...) ── Error ('test-regressions.R:195:5'): acti_calculate_counts passes only time/X/Y/Z to agcounts ── Error in `acti_standardize_epoch(epoch)`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics::acti_calculate_counts(...) at test-regressions.R:195:5 ── Error ('test-regressions.R:232:3'): fix_first_second_function pads to the epoch start robustly ── Error in `acti_standardize_epoch(epoch, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics:::fix_first_second_function(data, epoch = 60L) at test-regressions.R:232:3 2. └─lubridate::floor_date(t1, acti_standardize_epoch(epoch, output = "character")) 3. └─lubridate::is.POSIXct(unit) ── Error ('test-regressions.R:413:3'): acti_calculate_counts rounds XYZ with round_digits ── Error in `acti_standardize_epoch(epoch)`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics::acti_calculate_counts(...) at test-regressions.R:413:3 ── Error ('test-regressions.R:431:3'): epoch/unit arguments accept any acti_standardize_epoch() form ── Error: epoch is not a string (a length one character vector). Backtrace: ▆ 1. ├─testthat::expect_equal(n_in_interval(30, sample_rate = 10), 300) at test-regressions.R:431:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─actimetrics:::n_in_interval(30, sample_rate = 10) 5. └─assertthat::assert_that(assertthat::is.string(epoch)) ── Error ('test-step-walking.R:35:3'): stepcount wrapper uses the provided or inferred sample rate ── Error in `acti_standardize_epoch(epoch, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics::acti_calculate_stepcount(data) at test-step-walking.R:35:3 ── Error ('test-step-walking.R:90:5'): stepcount and sdt infer sample rate when missing ── Error in `acti_standardize_epoch(epoch, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-step-walking.R:89:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─actimetrics::acti_calculate_stepcount(data) at test-step-walking.R:90:5 ── Error ('test-step-walking.R:113:3'): summarize_to_minute aggregates step data ── Error in `acti_standardize_epoch(unit, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics:::summarize_to_minute(sdata, prefix = "test") at test-step-walking.R:113:3 ── Error ('test-step-walking.R:158:3'): walking wrappers summarize mocked step outputs ── Error in `acti_standardize_epoch(unit, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─actimetrics::acti_calculate_verisense(data, method = "revised") at test-step-walking.R:158:3 2. └─actimetrics:::summarize_to_minute(sdata, prefix = "acti_calculate_verisense") [ FAIL 14 | WARN 4 | SKIP 7 | PASS 153 ] Error: ! Test failures. Execution halted