* using log directory ‘/home/hornik/tmp/CRAN_pretest/actimetrics.Rcheck’ * using R Under development (unstable) (2026-10-19 r90720) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 23.1.0 (2) Debian flang version 23.1.0 (2) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-10-20 04:29:59 UTC * checking for file ‘actimetrics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘actimetrics’ version ‘0.9.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/6s] OK * 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 ‘actimetrics’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [5s/5s] NOTE acti_calculate_counts: no visible global function definition for ‘acti_standardize_epoch’ acti_calculate_stepcount: no visible global function definition for ‘acti_standardize_epoch’ fix_first_second_function: no visible global function definition for ‘acti_standardize_epoch’ summarize_to_minute: no visible global function definition for ‘acti_standardize_epoch’ Undefined global functions or variables: acti_standardize_epoch * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'acti_calculate_counts.Rd': ‘[actibase:acti_standardize_epoch]{actibase::acti_standardize_epoch()}’ Missing link(s) in Rd file 'acti_calculate_stepcount.Rd': ‘[actibase:acti_standardize_epoch]{actibase::acti_standardize_epoch()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [2s/2s] ERROR Running examples in ‘actimetrics-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: acti_calculate_sdt > ### Title: Calculate Step Counts via SDT > ### Aliases: acti_calculate_sdt > > ### ** Examples > > data = actiread::acti_read_gt3x(actiread::acti_example_gt3x()) Warning in feat[features] : object length is not a multiple of subscript length ℹ Filling zeros in data ✔ Filled zeros in data ℹ Timezone not applied to data > steps = acti_calculate_sdt(data) sdt completed Error in acti_standardize_epoch(unit, output = "character") : could not find function "acti_standardize_epoch" Calls: acti_calculate_sdt -> summarize_to_minute Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [93s/69s] ERROR Running ‘testthat.R’ [93s/69s] 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 matplotlib (11.0MiB) Downloading llvmlite (41.6MiB) Downloading numba (3.5MiB) Downloading transforms3d (1.3MiB) Downloading kiwisolver (1.6MiB) Downloading pillow (6.6MiB) Downloading nvidia-cudnn-cu11 (531.3MiB) Downloading nvidia-cuda-nvrtc-cu11 (20.0MiB) Downloading scipy (32.8MiB) Downloading pandas (11.7MiB) Downloading torchvision (23.1MiB) Downloading scikit-learn (29.0MiB) Downloading numpy (16.5MiB) Downloading nvidia-cublas-cu11 (302.4MiB) Downloading statsmodels (11.5MiB) Downloading fonttools (5.0MiB) Downloading torch (846.3MiB) Downloaded transforms3d Downloaded kiwisolver Downloaded numba Downloaded fonttools Downloaded pillow Downloaded matplotlib Downloaded statsmodels Downloaded pandas Downloaded numpy Downloaded nvidia-cuda-nvrtc-cu11 Downloaded torchvision Downloaded scipy Downloaded scikit-learn Downloaded llvmlite Downloaded nvidia-cublas-cu11 Downloaded nvidia-cudnn-cu11 Downloaded torch Installed 46 packages in 195ms Module(stepcount) > 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 Fixing Zeros with fix_zeros Flagging data Calculating ai0 Calculating MAD Joining AI and MAD Calculating MIMS Calculating AC Joining AC Joining MIMS Joining flags Detected gt3x file - reading in using acti_read_gt3x Filling Zeros 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 Saving _problems/test-stepcount-18.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 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 5 | SKIP 6 | PASS 160 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • 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' ══ 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-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") ── Error ('test-stepcount.R:18:7'): stepcount works ──────────────────────────── Error in `acti_standardize_epoch(epoch, output = "character")`: could not find function "acti_standardize_epoch" Backtrace: ▆ 1. └─base::tryCatch(...) at test-stepcount.R:11:3 2. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. └─value[[3L]](cond) [ FAIL 14 | WARN 5 | SKIP 6 | PASS 160 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [3s/4s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 1 NOTE