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eyeris

Flexible, Extensible, & Reproducible Pupillometry Preprocessing

v3.0.1 · Oct 7, 2025 · MIT + file LICENSE
CRAN GitHub Mirror

Description

Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the Stanford Wu Tsai Human Performance Alliance, Stanford Ric Weiland Graduate Fellowship, Stanford Center for Mind, Brain, Computation and Technology, NIH National Institute on Aging Grants (R01-AG065255, R01-AG079345), NSF GRFP (DGE-2146755), McKnight Brain Research Foundation Clinical Translational Research Scholarship in Cognitive Aging and Age-Related Memory Loss, American Brain Foundation, and the American Academy of Neurology.

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CRAN Check Status

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r-devel-macos-arm64 OK
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installed package size

              
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb

            

            

              

                NOTE
                r-oldrel-macos-x86_64
              

              
installed package size

              
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb

            

            

              

                NOTE
                r-oldrel-windows-x86_64
              

              
installed package size

              
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb

            

            

              

                ERROR
                r-oldrel-windows-x86_64
              

              
tests

              
  Running 'testthat.R' [122s]
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(eyeris)
  
  eyeris v3.0.1 - Lumpy Space Princess ꒰•ᴗ•｡꒱۶
  Welcome! Type ?`eyeris` to get started.
  
  > 
  > test_check("eyeris")
  i [2026-03-06 20:42:35] [INFO] Created output directory:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_chunked_output
  v [2026-03-06 20:42:35] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/bids_test/derivatives/test-db.eyerisdb
  i [2026-03-06 20:42:35] [INFO] Exporting data types: confounds_summary
  i [2026-03-06 20:42:35] [INFO] Processing data type: confounds_summary
  i [2026-03-06 20:42:35] [INFO] Grouping tables by epoch label...
  i [2026-03-06 20:42:36] [INFO] Found 1 epoch label groups for
  confounds_summary: _nolabel
  i [2026-03-06 20:42:36] [INFO] Analyzing column structures within epoch group
  '_nolabel'...
  i [2026-03-06 20:42:36] [INFO] Found 2 column-compatible groups within
  '_nolabel': goal, stim
  i [2026-03-06 20:42:36] [INFO] Processing confounds_summary group 'goal' (2
  tables)
  i [2026-03-06 20:42:36] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2026-03-06 20:42:36] [INFO] Processing with file size chunking enabled
  i [2026-03-06 20:42:36] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2026-03-06 20:42:36] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
  "confounds_summary_02_task_run01_goal"
  i [2026-03-06 20:42:36] [INFO] Processing chunk 1: 50 rows
  i [2026-03-06 20:42:36] [INFO] Created output file:
  test-db_confounds_summary_goal_chunked_01.csv
  i [2026-03-06 20:42:36] [INFO] Processing chunk 2: 50 rows
  i [2026-03-06 20:42:36] [INFO] Processing chunk 3: 50 rows
  i [2026-03-06 20:42:36] [INFO] No more data to process
  v [2026-03-06 20:42:36] [OKAY] Chunked processing complete:
  i [2026-03-06 20:42:36] [INFO] Total rows: 150
  i [2026-03-06 20:42:36] [INFO] Chunks: 3
  i [2026-03-06 20:42:36] [INFO] Processing time: 0 seconds
  i [2026-03-06 20:42:36] [INFO] Average rate: 4403 rows/second
  i [2026-03-06 20:42:36] [INFO] Processing confounds_summary group 'stim' (1
  tables)
  i [2026-03-06 20:42:36] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2026-03-06 20:42:36] [INFO] Processing with file size chunking enabled
  i [2026-03-06 20:42:36] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2026-03-06 20:42:36] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_stim"
  i [2026-03-06 20:42:36] [INFO] Processing chunk 1: 50 rows
  i [2026-03-06 20:42:36] [INFO] Created output file:
  test-db_confounds_summary_stim_chunked_01.csv
  i [2026-03-06 20:42:36] [INFO] Processing chunk 2: 50 rows
  i [2026-03-06 20:42:36] [INFO] No more data to process
  v [2026-03-06 20:42:36] [OKAY] Chunked processing complete:
  i [2026-03-06 20:42:36] [INFO] Total rows: 100
  i [2026-03-06 20:42:36] [INFO] Chunks: 2
  i [2026-03-06 20:42:36] [INFO] Processing time: 0 seconds
  i [2026-03-06 20:42:36] [INFO] Average rate: 4519 rows/second
  v [2026-03-06 20:42:36] [OKAY] Export complete!
  i [2026-03-06 20:42:36] [INFO] Data types exported: 2
  i [2026-03-06 20:42:36] [INFO] Total rows exported: 250
  i [2026-03-06 20:42:36] [INFO] Output directory:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_chunked_output
  i [2026-03-06 20:42:36] [INFO] Disconnected from eyeris database
  i [2026-03-06 20:42:36] [INFO] Created output directory:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/size_test_output
  v [2026-03-06 20:42:36] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/bids_size_test/derivatives/size-test.eyerisdb
  i [2026-03-06 20:42:37] [INFO] Exporting data types: timeseries
  i [2026-03-06 20:42:37] [INFO] Processing data type: timeseries
  i [2026-03-06 20:42:37] [INFO] Processing timeseries group 'all' (1 tables)
  i [2026-03-06 20:42:37] [INFO] Using chunked processing (file size limit =
  0.05MB < 500MB threshold)
  i [2026-03-06 20:42:37] [INFO] Processing with file size chunking enabled
  i [2026-03-06 20:42:37] [INFO] Starting chunked query processing (chunk size:
  500)
  i [2026-03-06 20:42:37] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
  i [2026-03-06 20:42:37] [INFO] Processing chunk 1: 500 rows
  i [2026-03-06 20:42:37] [INFO] Created output file:
  size-test_timeseries_chunked_01.csv
  i [2026-03-06 20:42:37] [INFO] Processing chunk 2: 500 rows
  i [2026-03-06 20:42:37] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_02.csv
  i [2026-03-06 20:42:37] [INFO] Created output file:
  size-test_timeseries_chunked_02.csv
  i [2026-03-06 20:42:37] [INFO] Processing chunk 3: 500 rows
  i [2026-03-06 20:42:37] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_03.csv
  i [2026-03-06 20:42:37] [INFO] Created output file:
  size-test_timeseries_chunked_03.csv
  i [2026-03-06 20:42:37] [INFO] Processing chunk 4: 500 rows
  i [2026-03-06 20:42:37] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_04.csv
  i [2026-03-06 20:42:37] [INFO] Created output file:
  size-test_timeseries_chunked_04.csv
  i [2026-03-06 20:42:37] [INFO] No more data to process
  v [2026-03-06 20:42:37] [OKAY] Chunked processing complete:
  i [2026-03-06 20:42:37] [INFO] Total rows: 2000
  i [2026-03-06 20:42:37] [INFO] Chunks: 4
  i [2026-03-06 20:42:37] [INFO] Processing time: 0.2 seconds
  i [2026-03-06 20:42:37] [INFO] Average rate: 12812 rows/second
  i [2026-03-06 20:42:37] [INFO] Finalizing 4 output files with proper
  numbering...
  i [2026-03-06 20:42:37] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
  size-test_timeseries_chunked_01-of-04.csv
  i [2026-03-06 20:42:37] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
  size-test_timeseries_chunked_02-of-04.csv
  i [2026-03-06 20:42:37] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
  size-test_timeseries_chunked_03-of-04.csv
  i [2026-03-06 20:42:37] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
  size-test_timeseries_chunked_04-of-04.csv
  v [2026-03-06 20:42:37] [OKAY] Export complete!
  i [2026-03-06 20:42:37] [INFO] Data types exported: 1
  i [2026-03-06 20:42:37] [INFO] Total rows exported: 2000
  i [2026-03-06 20:42:37] [INFO] Output directory:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/size_test_output
  i [2026-03-06 20:42:37] [INFO] Disconnected from eyeris database
  v [2026-03-06 20:42:39] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_bids/derivatives/user-test.eyerisdb
  i [2026-03-06 20:42:39] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  i [2026-03-06 20:42:39] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  AND session_id = '02' AND task_name = 'memory'
  i [2026-03-06 20:42:39] [INFO] Disconnected from eyeris database
  i [2026-03-06 20:42:41] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
  1=1 AND subject_id = '005'
  v [2026-03-06 20:42:42] [OKAY] Running eyeris::load_asc()
  i [2026-03-06 20:42:43] [INFO] Processing block: block_1
  v [2026-03-06 20:42:43] [OKAY] Running eyeris::deblink() for block_1
  v [2026-03-06 20:42:43] [OKAY] Running eyeris::detransient() for block_1
  v [2026-03-06 20:42:43] [OKAY] Running eyeris::interpolate() for block_1
  v [2026-03-06 20:42:43] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2026-03-06 20:42:43] [WARN] Skipping eyeris::downsample() for block_1
  ! [2026-03-06 20:42:43] [WARN] Skipping eyeris::bin() for block_1
  ! [2026-03-06 20:42:43] [WARN] Skipping eyeris::detrend() for block_1
  v [2026-03-06 20:42:43] [OKAY] Running eyeris::zscore() for block_1
  i [2026-03-06 20:42:43] [INFO] Block processing summary:
  i [2026-03-06 20:42:43] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2026-03-06 20:42:43] [OKAY] Running eyeris::summarize_confounds()
  i [2026-03-06 20:42:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:42:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2026-03-06 20:43:07] [WARN] No detrend data found for run-01
  
  
  processing file: sub-001.Rmd
  output file: sub-001.knit.md
  
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css "D:/RCompile/CRANpkg/lib/4.4/eyeris/rmarkdown/css/report.css" --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE\rmarkdown-str68d472252a60.html" 
  File  not found in resource path
  Saving _problems/test-parallel-database-21.R
  v [2026-03-06 20:43:08] [OKAY] Running eyeris::load_asc()
  i [2026-03-06 20:43:08] [INFO] Processing block: block_1
  v [2026-03-06 20:43:08] [OKAY] Running eyeris::deblink() for block_1
  v [2026-03-06 20:43:09] [OKAY] Running eyeris::detransient() for block_1
  v [2026-03-06 20:43:09] [OKAY] Running eyeris::interpolate() for block_1
  v [2026-03-06 20:43:09] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2026-03-06 20:43:09] [WARN] Skipping eyeris::downsample() for block_1
  ! [2026-03-06 20:43:09] [WARN] Skipping eyeris::bin() for block_1
  ! [2026-03-06 20:43:09] [WARN] Skipping eyeris::detrend() for block_1
  v [2026-03-06 20:43:09] [OKAY] Running eyeris::zscore() for block_1
  i [2026-03-06 20:43:09] [INFO] Block processing summary:
  i [2026-03-06 20:43:09] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2026-03-06 20:43:09] [OKAY] Running eyeris::summarize_confounds()
  i [2026-03-06 20:43:11] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2026-03-06 20:43:32] [WARN] No detrend data found for run-01
  
  
  processing file: sub-002.Rmd
  output file: sub-002.knit.md
  
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css "D:/RCompile/CRANpkg/lib/4.4/eyeris/rmarkdown/css/report.css" --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE\rmarkdown-str68d4178b6eb0.html" 
  File  not found in resource path
  Saving _problems/test-parallel-database-42.R
  v [2026-03-06 20:43:33] [OKAY] Running eyeris::load_asc()
  i [2026-03-06 20:43:33] [INFO] Processing block: block_1
  v [2026-03-06 20:43:33] [OKAY] Running eyeris::deblink() for block_1
  v [2026-03-06 20:43:33] [OKAY] Running eyeris::detransient() for block_1
  v [2026-03-06 20:43:33] [OKAY] Running eyeris::interpolate() for block_1
  v [2026-03-06 20:43:33] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2026-03-06 20:43:34] [WARN] Skipping eyeris::downsample() for block_1
  ! [2026-03-06 20:43:34] [WARN] Skipping eyeris::bin() for block_1
  ! [2026-03-06 20:43:34] [WARN] Skipping eyeris::detrend() for block_1
  v [2026-03-06 20:43:34] [OKAY] Running eyeris::zscore() for block_1
  i [2026-03-06 20:43:34] [INFO] Block processing summary:
  i [2026-03-06 20:43:34] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2026-03-06 20:43:34] [OKAY] Running eyeris::summarize_confounds()
  i [2026-03-06 20:43:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:43:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2026-03-06 20:43:56] [WARN] No detrend data found for run-01
  
  
  processing file: sub-003.Rmd
  output file: sub-003.knit.md
  
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css "D:/RCompile/CRANpkg/lib/4.4/eyeris/rmarkdown/css/report.css" --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE\rmarkdown-str68d4125b7666.html" 
  File  not found in resource path
  Saving _problems/test-parallel-database-62.R
  v [2026-03-06 20:43:57] [OKAY] Running eyeris::load_asc()
  i [2026-03-06 20:43:57] [INFO] Processing block: block_1
  v [2026-03-06 20:43:57] [OKAY] Running eyeris::deblink() for block_1
  v [2026-03-06 20:43:57] [OKAY] Running eyeris::detransient() for block_1
  v [2026-03-06 20:43:58] [OKAY] Running eyeris::interpolate() for block_1
  v [2026-03-06 20:43:58] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2026-03-06 20:43:58] [WARN] Skipping eyeris::downsample() for block_1
  ! [2026-03-06 20:43:58] [WARN] Skipping eyeris::bin() for block_1
  ! [2026-03-06 20:43:58] [WARN] Skipping eyeris::detrend() for block_1
  v [2026-03-06 20:43:58] [OKAY] Running eyeris::zscore() for block_1
  i [2026-03-06 20:43:58] [INFO] Block processing summary:
  i [2026-03-06 20:43:58] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2026-03-06 20:43:58] [OKAY] Running eyeris::summarize_confounds()
  i [2026-03-06 20:44:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:11] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2026-03-06 20:44:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2026-03-06 20:44:21] [WARN] No detrend data found for run-01
  
  
  processing file: sub-004.Rmd
  output file: sub-004.knit.md
  
  "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.4\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css "D:/RCompile/CRANpkg/lib/4.4/eyeris/rmarkdown/css/report.css" --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE\rmarkdown-str68d479cf1fe4.html" 
  File  not found in resource path
  Saving _problems/test-parallel-database-82.R
  i [2026-03-06 20:44:24] [INFO] Disconnected from eyeris database
  v [2026-03-06 20:44:24] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_bids/derivatives/test-study.eyerisdb
  i [2026-03-06 20:44:24] [INFO] Disconnected from eyeris database
  i [2026-03-06 20:44:25] [INFO] Disconnected from eyeris database
  v [2026-03-06 20:44:25] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_bids_read/derivatives/read-test.eyerisdb
  i [2026-03-06 20:44:25] [INFO] Disconnected from eyeris database
  i [2026-03-06 20:44:26] [INFO] Disconnected from eyeris database
  v [2026-03-06 20:44:26] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_bids_size/derivatives/size-test.eyerisdb
  i [2026-03-06 20:44:26] [INFO] Disconnected from eyeris database
  i [2026-03-06 20:44:26] [INFO] Disconnected from eyeris database
  v [2026-03-06 20:44:26] [OKAY] Connected to eyeris database:
  D:\temp\2026_03_06_01_50_00_25361\RtmpIxqaoE/test_bids_empty/derivatives/empty-test.eyerisdb
  ! [2026-03-06 20:44:26] [WARN] No valid tables found in database (after
  excluding temp tables)
  i [2026-03-06 20:44:27] [INFO] Disconnected from eyeris database
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::load_asc()
  i [2026-03-06 20:44:27] [INFO] Processing block: block_1
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::deblink() for block_1
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::detransient() for block_1
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::interpolate() for block_1
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2026-03-06 20:44:27] [WARN] Skipping eyeris::downsample() for block_1
  ! [2026-03-06 20:44:27] [WARN] Skipping eyeris::bin() for block_1
  ! [2026-03-06 20:44:27] [WARN] Skipping eyeris::detrend() for block_1
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::zscore() for block_1
  i [2026-03-06 20:44:27] [INFO] Block processing summary:
  i [2026-03-06 20:44:27] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2026-03-06 20:44:27] [OKAY] Running eyeris::summarize_confounds()
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::load_asc()
  i [2026-03-06 20:44:28] [INFO] Binocular data detected. Processing average
  mode.
  i [2026-03-06 20:44:28] [INFO] Processing block: block_1
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::deblink() for block_1
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::detransient() for block_1
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::interpolate() for block_1
  ! [2026-03-06 20:44:28] [WARN] No NAs detected in pupil data... Skipping
  interpolation!
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2026-03-06 20:44:28] [WARN] Skipping eyeris::downsample() for block_1
  ! [2026-03-06 20:44:28] [WARN] Skipping eyeris::bin() for block_1
  ! [2026-03-06 20:44:28] [WARN] Skipping eyeris::detrend() for block_1
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::zscore() for block_1
  i [2026-03-06 20:44:28] [INFO] Block processing summary:
  i [2026-03-06 20:44:28] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2026-03-06 20:44:28] [OKAY] Running eyeris::summarize_confounds()
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 188 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-parallel-database.R:9:5'): manual parallel processing flag enables temporary databases ──
  Expected `{ ... }` not to throw any errors.
  Actually got a <simpleError> with message:
    pandoc document conversion failed with error 99
  Backtrace:
      ▆
   1. ├─withr::with_envvar(...) at test-parallel-database.R:4:3
   2. │ └─base::force(code)
   3. └─testthat::expect_no_error(...) at test-parallel-database.R:9:5
  ── Failure ('test-parallel-database.R:31:5'): SLURM environment variables are detected for parallel processing ──
  Expected `{ ... }` not to throw any errors.
  Actually got a <simpleError> with message:
    pandoc document conversion failed with error 99
  Backtrace:
      ▆
   1. ├─withr::with_envvar(...) at test-parallel-database.R:28:3
   2. │ └─base::force(code)
   3. └─testthat::expect_no_error(...) at test-parallel-database.R:31:5
  ── Failure ('test-parallel-database.R:51:5'): PBS environment variables are detected for parallel processing ──
  Expected `{ ... }` not to throw any errors.
  Actually got a <simpleError> with message:
    pandoc document conversion failed with error 99
  Backtrace:
      ▆
   1. ├─withr::with_envvar(...) at test-parallel-database.R:48:3
   2. │ └─base::force(code)
   3. └─testthat::expect_no_error(...) at test-parallel-database.R:51:5
  ── Failure ('test-parallel-database.R:70:3'): normal database operation works without parallel processing ──
  Expected `{ ... }` not to throw any errors.
  Actually got a <simpleError> with message:
    pandoc document conversion failed with error 99
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 188 ]
  Error:
  ! Test failures.
  Execution halted

            

            

              

                OK
                r-patched-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-macos-arm64
              

              
*

              

            

            

              

                OK
                r-release-macos-x86_64
              

              
*

              

            

            

              

                OK
                r-release-windows-x86_64
              

              
*

              

            

          

        

      



      

      
      

        
Check History

        

          

            
              ERROR
              
                11 OK ·                 2 NOTE ·                 0 WARNING ·                 1 ERROR ·                 0 FAILURE              
              Mar 9, 2026
            
            

              

                

                  NOTE
                  r-oldrel-macos-arm64
                

                
installed package size

                
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb

              

              

                

                  NOTE
                  r-oldrel-macos-x86_64
                

                
installed package size

                
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb

              

              

                

                  ERROR
                  r-oldrel-windows-x86_64
                

                
installed package size

                
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb

              

            

          

        

      


      

      
      

        
Dependency Network

        

          
            

            
            
            Dependencies
            
            Reverse dependencies

            
            
            
            
            
            
            
            
            
            
            
            
            
            
            
            

            

            
            
              
              eyelinker
            
            
              
              dplyr
            
            
              
              gsignal
            
            
              
              purrr
            
            
              
              zoo
            
            
              
              cli
            
            
              
              rlang
            
            
              
              stringr
            
            
              
              tidyr
            
            
              
              progress
            
            
              
              data.table
            
            
              
              withr
            
            
              
              lifecycle
            
            
              
              MASS
            
            
              
              viridis
            
            +6 more dependencies

            

            
            
            eyeris
          
        

      


      
      

        
Version History

        

          

            new
            3.0.1
            Mar 9, 2026