• using R version 4.5.2 Patched (2026-01-31 r89382)
• using platform: aarch64-apple-darwin20
• R was compiled by     Apple clang version 16.0.0 (clang-1600.0.26.6)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.7.8
• using session charset: UTF-8
• checking for file ‘wrictools/DESCRIPTION’ ... OK
• this is package ‘wrictools’ version ‘1.0.1’
• 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 ‘wrictools’ can be installed ... [2s/2s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... 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 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 ... [2s/2s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/3s] ERROR   Running ‘testthat.R’ [3s/3s] 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(wrictools)   >   > test_check("wrictools")   Starting time for room 1 is 2023-11-13 21:14:22 and end 2023-11-14 08:47:48 and for room 2 start is 2023-11-13 21:14:22 and end 2023-11-14 08:51:36   Starting time for room 1 is 2023-11-13 21:14:22 and end 2023-11-14 08:47:48 and for room 2 start is 2023-11-13 21:14:22 and end 2023-11-14 08:51:36   Saving _problems/test-processing-416.R     variable mean sd min max slope   1 VO2 356.7205 100.54488 -29.90960 786.6187 0.002766024   2 VCO2 298.4697 87.95359 -45.17043 674.9738 0.002499467     variable mean sd min max slope   1 VO2 332.0050 122.09571 -500.9322 708.2423 0.001944661   2 VCO2 267.9337 99.32789 -413.3808 565.4705 0.001476097     variable mean sd min max slope   1 VO2 47.500000 7.745967 30 62 -0.0096304348   2 VCO2 8.791667 1.052086 7 10 -0.0005289855   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-processing.R:416:3'): extract_protocol_events works for old and new software ──   Expected `as.character(first_entry_v2$timestamp)` to equal "2026-01-14 11:58:01".   Differences:   `actual`: "2026-01-13 11:58:01"   `expected`: "2026-01-14 11:58:01"         [ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [7s/7s] ERROR Error(s) in re-building vignettes: --- re-building ‘RedCAP.Rmd’ using rmarkdown --- finished re-building ‘RedCAP.Rmd’ --- re-building ‘test_analysis.Rmd’ using rmarkdown 2026-05-08 13:49:21.822 R[73461:434235] XType: Using static font registry. --- finished re-building ‘test_analysis.Rmd’ --- re-building ‘wrictools.Rmd’ using rmarkdown preprocess_wric_file package:wrictools R Documentation _ P_ r_ e_ p_ r_ o_ c_ e_ s_ s_ e_ s _ a _ w_ r_ i_ c _ d_ a_ t_ a _ f_ i_ l_ e, _ e_ x_ t_ r_ a_ c_ t_ i_ n_ g _ m_ e_ t_ a_ d_ a_ t_ a, _ c_ r_ e_ a_ t_ i_ n_ g _ D_ a_ t_ a_ F_ r_ a_ m_ e_ s, _ a_ n_ d _ o_ p_ t_ i_ o_ n_ a_ l_ l_ y _ s_ a_ v_ i_ n_ g _ r_ e_ s_ u_ l_ t_ s. _ D_ e_ s_ c_ r_ i_ p_ t_ i_ o_ n:      Preprocesses a wric data file, extracting metadata, creating      DataFrames, and optionally saving results. _ U_ s_ a_ g_ e:      preprocess_wric_file(        filepath,        code = "id",        manual = NULL,        save_csv = FALSE,        path_to_save = NULL,        combine = TRUE,        method = "mean",        start = NULL,        end = NULL,        notefilepath = NULL,        keywords_dict = NULL,        entry_exit_dict = NULL      )       _ A_ r_ g_ u_ m_ e_ n_ t_ s: filepath: Path to the wric .txt file.     code: Method for generating subject IDs ("id", "id+comment",           "study+id" (only for software v2), or "manual").   manual: Custom codes for subjects in Room 1 and Room 2 if 'code' is           "manual". save_csv: Logical, whether to save extracted metadata and data to CSV           files. path_to_save: Directory path for saving CSV files, NULL uses the           current directory.  combine: Logical, whether to combine S1 and S2 measurements.   method: Method for combining measurements ("mean", "median", "s1",           "s2", "min", "max").    start: character or POSIXct or NULL, rows before this will be           removed, if NULL takes first row e.g "2023-11-13 11:43:00"      end: character or POSIXct or NULL, rows after this will be           removed, if NULL takes last row e.g "2023-11-13 11:43:00" notefilepath: String, Directory path of the corresponding note file           (.txt) keywords_dict: List, A dictionary of keywords used to extract protocol           events from a note file. Each entry should be a named list           with:           keywords A character vector of keywords or phrases to match               in the note comment. Matching is case-insensitive.           value Numeric protocol value to assign when the keyword is               detected.           type Optional character, either "instant" or omitted.               "instant" events are applied at the specified timestamp               and revert to the previous protocol immediately after.               Non-instant events set the protocol until another event               occurs.           Behavior rules:           Non-instant events Set the protocol value from their               timestamp until another event overwrites it or until a               stop keyword sets it to 0.           Instant events Apply only at the timestamp of the note line,               then revert to the protocol that was active immediately               before.           Stop keywords Always set the protocol to 0, regardless of               previous state, unless overridden by an instant event.           If 'NULL', a default set of keywords is used. entry_exit_dict: Nested List, used to extract entry/exit times from           note file _ V_ a_ l_ u_ e:      list A list with the following components:      version Character string indicating the detected software version           ('"1"' for old software, '"2"' for new software).      metadata A named list containing extracted metadata. For version           1, this includes 'r1' and 'r2'. For version 2, this contains           a single 'metadata' entry.      dfs A named list containing processed data frames. For version 1:           'room1' and 'room2'. For version 2: 'data'. _ E_ x_ a_ m_ p_ l_ e_ s:      outdir <- file.path(tempdir(), "wrictools")      dir.create(outdir, showWarnings = FALSE)      data_txt <- system.file("extdata", "data.txt", package = "wrictools")      result <- preprocess_wric_file(data_txt, path_to_save = outdir)      unlink(outdir, recursive = TRUE)       Quitting from wrictools.Rmd:312-319 [unnamed-chunk-19] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `dinner_index:(dinner_index + 14)`: ! NA/NaN argument --- Backtrace:     ▆  1. ├─data[dinner_index:(dinner_index + 14), ]  2. └─base::`[.data.frame`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'wrictools.Rmd' failed with diagnostics: NA/NaN argument --- failed re-building ‘wrictools.Rmd’ SUMMARY: processing the following file failed:   ‘wrictools.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [2s/2s] OK
• DONE Status: 2 ERRORs
• using check arguments '--no-clean-on-error '