Last updated on 2026-11-09 01:52:15 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.3.0 | 14.63 | 410.31 | 424.94 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.3.0 | 9.67 | 284.72 | 294.39 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.3.0 | 11.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.3.0 | 10.00 | 283.21 | 293.21 | OK | |
| r-devel-windows-x86_64 | 3.3.0 | 25.00 | 441.00 | 466.00 | OK | |
| r-patched-linux-x86_64 | 3.3.0 | OK | ||||
| r-release-linux-x86_64 | 3.3.0 | 11.94 | 388.36 | 400.30 | OK | |
| r-release-macos-arm64 | 3.3.0 | 4.00 | 102.00 | 106.00 | OK | |
| r-release-macos-x86_64 | 3.3.0 | 12.00 | 423.00 | 435.00 | OK | |
| r-release-windows-x86_64 | 3.3.0 | 25.00 | 450.00 | 475.00 | OK | |
| r-oldrel-macos-arm64 | 3.3.0 | 4.00 | 108.00 | 112.00 | OK | |
| r-oldrel-macos-x86_64 | 3.3.0 | 12.00 | 634.00 | 646.00 | OK | |
| r-oldrel-windows-x86_64 | 3.3.0 | 30.00 | 591.00 | 621.00 | OK |
Version: 3.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [130s/151s]
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 v3.3.0 - Lumpy Space Princess ꒰•ᴗ•｡꒱۶
Welcome! Type ?`eyeris` to get started.
>
> test_check("eyeris")
! [2026-11-08 17:18:46] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
Saving _problems/test-chunked-processing-200.R
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:18:53] [INFO] Created output directory:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_chunked_output
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:18:53] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/bids_test/derivatives/test-db.eyerisdb
i [2026-11-08 17:18:53] [INFO] Exporting data types: confounds_summary
i [2026-11-08 17:18:53] [INFO] Processing data type: confounds_summary
i [2026-11-08 17:18:53] [INFO] Grouping tables by epoch label...
i [2026-11-08 17:18:53] [INFO] Found 1 epoch label groups for
confounds_summary: _nolabel
i [2026-11-08 17:18:53] [INFO] Analyzing column structures within epoch group
'_nolabel'...
i [2026-11-08 17:18:53] [INFO] Found 2 column-compatible groups within
'_nolabel': goal, stim
i [2026-11-08 17:18:53] [INFO] Processing confounds_summary group 'goal' (2
tables)
i [2026-11-08 17:18:53] [INFO] Using chunked processing (file size limit = 50MB
< 500MB threshold)
i [2026-11-08 17:18:53] [INFO] Processing with file size chunking enabled
i [2026-11-08 17:18:53] [INFO] Starting chunked query processing (chunk size:
50)
i [2026-11-08 17:18:53] [INFO] Query: SELECT * FROM
"confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
"confounds_summary_02_task_run01_goal"
i [2026-11-08 17:18:53] [INFO] Processing chunk 1: 50 rows
i [2026-11-08 17:18:53] [INFO] Created output file:
test-db_confounds_summary_goal_chunked_01.csv
i [2026-11-08 17:18:53] [INFO] Processing chunk 2: 50 rows
i [2026-11-08 17:18:53] [INFO] Processing chunk 3: 50 rows
i [2026-11-08 17:18:53] [INFO] No more data to process
v [2026-11-08 17:18:53] [OKAY] Chunked processing complete:
i [2026-11-08 17:18:53] [INFO] Total rows: 150
i [2026-11-08 17:18:53] [INFO] Chunks: 3
i [2026-11-08 17:18:53] [INFO] Processing time: 0 seconds
i [2026-11-08 17:18:53] [INFO] Average rate: 7009 rows/second
i [2026-11-08 17:18:53] [INFO] Processing confounds_summary group 'stim' (1
tables)
i [2026-11-08 17:18:53] [INFO] Using chunked processing (file size limit = 50MB
< 500MB threshold)
i [2026-11-08 17:18:53] [INFO] Processing with file size chunking enabled
i [2026-11-08 17:18:53] [INFO] Starting chunked query processing (chunk size:
50)
i [2026-11-08 17:18:53] [INFO] Query: SELECT * FROM
"confounds_summary_01_task_run01_stim"
i [2026-11-08 17:18:53] [INFO] Processing chunk 1: 50 rows
i [2026-11-08 17:18:53] [INFO] Created output file:
test-db_confounds_summary_stim_chunked_01.csv
i [2026-11-08 17:18:53] [INFO] Processing chunk 2: 50 rows
i [2026-11-08 17:18:53] [INFO] No more data to process
v [2026-11-08 17:18:53] [OKAY] Chunked processing complete:
i [2026-11-08 17:18:53] [INFO] Total rows: 100
i [2026-11-08 17:18:53] [INFO] Chunks: 2
i [2026-11-08 17:18:53] [INFO] Processing time: 0 seconds
i [2026-11-08 17:18:53] [INFO] Average rate: 5911 rows/second
v [2026-11-08 17:18:53] [OKAY] Export complete!
i [2026-11-08 17:18:53] [INFO] Data types exported: 2
i [2026-11-08 17:18:53] [INFO] Total rows exported: 250
i [2026-11-08 17:18:53] [INFO] Output directory:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_chunked_output
i [2026-11-08 17:18:53] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:18:54] [INFO] Created output directory:
/home/hornik/tmp/scratch/RtmpPJbS1W/size_test_output
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:18:54] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/bids_size_test/derivatives/size-test.eyerisdb
i [2026-11-08 17:18:54] [INFO] Exporting data types: timeseries
i [2026-11-08 17:18:54] [INFO] Processing data type: timeseries
i [2026-11-08 17:18:54] [INFO] Processing timeseries group 'all' (1 tables)
i [2026-11-08 17:18:54] [INFO] Using chunked processing (file size limit =
0.05MB < 500MB threshold)
i [2026-11-08 17:18:54] [INFO] Processing with file size chunking enabled
i [2026-11-08 17:18:54] [INFO] Starting chunked query processing (chunk size:
500)
i [2026-11-08 17:18:54] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
i [2026-11-08 17:18:54] [INFO] Processing chunk 1: 500 rows
i [2026-11-08 17:18:54] [INFO] Created output file:
size-test_timeseries_chunked_01.csv
i [2026-11-08 17:18:54] [INFO] Processing chunk 2: 500 rows
i [2026-11-08 17:18:54] [INFO] Starting new file due to size limit:
size-test_timeseries_chunked_02.csv
i [2026-11-08 17:18:54] [INFO] Created output file:
size-test_timeseries_chunked_02.csv
i [2026-11-08 17:18:54] [INFO] Processing chunk 3: 500 rows
i [2026-11-08 17:18:54] [INFO] Starting new file due to size limit:
size-test_timeseries_chunked_03.csv
i [2026-11-08 17:18:54] [INFO] Created output file:
size-test_timeseries_chunked_03.csv
i [2026-11-08 17:18:54] [INFO] Processing chunk 4: 500 rows
i [2026-11-08 17:18:54] [INFO] Starting new file due to size limit:
size-test_timeseries_chunked_04.csv
i [2026-11-08 17:18:54] [INFO] Created output file:
size-test_timeseries_chunked_04.csv
i [2026-11-08 17:18:54] [INFO] No more data to process
v [2026-11-08 17:18:54] [OKAY] Chunked processing complete:
i [2026-11-08 17:18:54] [INFO] Total rows: 2000
i [2026-11-08 17:18:54] [INFO] Chunks: 4
i [2026-11-08 17:18:54] [INFO] Processing time: 0.1 seconds
i [2026-11-08 17:18:54] [INFO] Average rate: 38721 rows/second
i [2026-11-08 17:18:54] [INFO] Finalizing 4 output files with proper
numbering...
i [2026-11-08 17:18:54] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
size-test_timeseries_chunked_01-of-04.csv
i [2026-11-08 17:18:54] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
size-test_timeseries_chunked_02-of-04.csv
i [2026-11-08 17:18:54] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
size-test_timeseries_chunked_03-of-04.csv
i [2026-11-08 17:18:54] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
size-test_timeseries_chunked_04-of-04.csv
v [2026-11-08 17:18:54] [OKAY] Export complete!
i [2026-11-08 17:18:54] [INFO] Data types exported: 1
i [2026-11-08 17:18:54] [INFO] Total rows exported: 2000
i [2026-11-08 17:18:54] [INFO] Output directory:
/home/hornik/tmp/scratch/RtmpPJbS1W/size_test_output
i [2026-11-08 17:18:54] [INFO] Disconnected from eyeris database
v [2026-11-08 17:18:54] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:18:54] [OKAY] Running eyeris::resample()
i [2026-11-08 17:18:54] [INFO] Processing block: block_1
v [2026-11-08 17:18:54] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:18:54] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:18:55] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:18:55] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:18:55] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:18:55] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:18:55] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:18:55] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:18:55] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:18:55] [INFO] Block processing summary:
i [2026-11-08 17:18:55] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:18:55] [OKAY] Running eyeris::summarize_confounds()
v [2026-11-08 17:18:55] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:18:55] [OKAY] Running eyeris::resample()
i [2026-11-08 17:18:55] [INFO] Processing block: block_1
v [2026-11-08 17:18:55] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:18:55] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:18:55] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:18:55] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:18:55] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:18:55] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:18:55] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:18:55] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:18:55] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:18:55] [INFO] Block processing summary:
i [2026-11-08 17:18:55] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:18:55] [OKAY] Running eyeris::summarize_confounds()
v [2026-11-08 17:18:55] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:18:56] [OKAY] Running eyeris::resample()
i [2026-11-08 17:18:56] [INFO] Processing block: block_1
v [2026-11-08 17:18:56] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:18:56] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:18:56] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:18:56] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:18:56] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:18:56] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:18:56] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:18:56] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:18:56] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:18:56] [INFO] Block processing summary:
i [2026-11-08 17:18:56] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:18:56] [OKAY] Running eyeris::summarize_confounds()
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:18:59] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_bids/derivatives/user-test.eyerisdb
i [2026-11-08 17:18:59] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"created_timestamp", "pupil_raw", "matched_event" FROM
"epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
i [2026-11-08 17:18:59] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"created_timestamp", "pupil_raw", "matched_event" 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 [2026-11-08 17:18:59] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:19:01] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"epoch_label", "created_timestamp", "pupil_raw", "matched_event" FROM
"epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
1=1 AND subject_id = '005'
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:19:01] [INFO] Detected 2 differing column schemas across 2
'run_confounds' tables; aligning columns and filling missing values with NA.
i [2026-11-08 17:19:01] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"created_timestamp", "blink_count", NULL AS "n_missing", NULL AS "prop_missing"
FROM "run_confounds_010_01_test_run01" UNION ALL SELECT "subject_id",
"session_id", "task_name", "data_type", "run_number", "created_timestamp",
"blink_count", "n_missing", "prop_missing" FROM
"run_confounds_011_01_test_run01") as combined_data WHERE 1=1
i [2026-11-08 17:19:01] [INFO] Detected 2 differing column schemas across 2
'run_confounds' tables; aligning columns and filling missing values with NA.
i [2026-11-08 17:19:01] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"created_timestamp", "blink_count", NULL AS "n_missing", NULL AS "prop_missing"
FROM "run_confounds_010_01_test_run01" UNION ALL SELECT "subject_id",
"session_id", "task_name", "data_type", "run_number", "created_timestamp",
"blink_count", "n_missing", "prop_missing" FROM
"run_confounds_011_01_test_run01") as combined_data WHERE 1=1 AND subject_id =
'010'
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:19:02] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_bids/derivatives/collect-sch.eyerisdb
i [2026-11-08 17:19:02] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"epoch_label", "created_timestamp", "blink_count" FROM
"confounds_events_012_01_test_run01_labela") as combined_data WHERE 1=1
i [2026-11-08 17:19:02] [INFO] Executing query: SELECT * FROM (SELECT
"subject_id", "session_id", "task_name", "data_type", "run_number",
"epoch_label", "created_timestamp", "blink_count", "prop_missing" FROM
"confounds_events_013_01_test_run01_labelb") as combined_data WHERE 1=1
i [2026-11-08 17:19:02] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:19:02] [INFO] Detected 2 differing column schemas across 2
'qtest' tables; aligning columns and filling missing values with NA.
i [2026-11-08 17:19:02] [INFO] Executing query: SELECT * FROM (SELECT
"wei""rd", "subject_id", NULL AS "extra" FROM "qtest_020_01_test_run01" UNION
ALL SELECT "wei""rd", "subject_id", "extra" FROM "qtest_021_01_test_run01") as
combined_data WHERE 1=1
! [2026-11-08 17:19:07] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
! [2026-11-08 17:19:11] [WARN] `lpfilt()` is operating on data that contains
gaps longer than the interpolation limit (`max_gap_ms`), which were left as
`NA`. These gaps are temporarily filled so the filter can run and then masked
back to `NA`; this can slightly bias the valid pupil samples immediately
adjacent to each gap toward the interpolated values. If this bias is a concern
for your analysis, consider disabling filtering and/or downsampling (e.g.
`lpfilt = FALSE` and/or `downsample = FALSE` in `glassbox()`).
! [2026-11-08 17:19:12] [WARN] `downsample()` is operating on data that
contains gaps longer than the interpolation limit (`max_gap_ms`), which were
left as `NA`. These gaps are temporarily filled so the filter can run and then
masked back to `NA`; this can slightly bias the valid pupil samples immediately
adjacent to each gap toward the interpolated values. If this bias is a concern
for your analysis, consider disabling filtering and/or downsampling (e.g.
`lpfilt = FALSE` and/or `downsample = FALSE` in `glassbox()`).
! [2026-11-08 17:19:14] [WARN] `lpfilt()` is operating on data that contains
gaps longer than the interpolation limit (`max_gap_ms`), which were left as
`NA`. These gaps are temporarily filled so the filter can run and then masked
back to `NA`; this can slightly bias the valid pupil samples immediately
adjacent to each gap toward the interpolated values. If this bias is a concern
for your analysis, consider disabling filtering and/or downsampling (e.g.
`lpfilt = FALSE` and/or `downsample = FALSE` in `glassbox()`).
! [2026-11-08 17:19:14] [WARN] `downsample()` is operating on data that
contains gaps longer than the interpolation limit (`max_gap_ms`), which were
left as `NA`. These gaps are temporarily filled so the filter can run and then
masked back to `NA`; this can slightly bias the valid pupil samples immediately
adjacent to each gap toward the interpolated values. If this bias is a concern
for your analysis, consider disabling filtering and/or downsampling (e.g.
`lpfilt = FALSE` and/or `downsample = FALSE` in `glassbox()`).
! [2026-11-08 17:19:15] [WARN] `lpfilt()` is operating on data that contains
gaps longer than the interpolation limit (`max_gap_ms`), which were left as
`NA`. These gaps are temporarily filled so the filter can run and then masked
back to `NA`; this can slightly bias the valid pupil samples immediately
adjacent to each gap toward the interpolated values. If this bias is a concern
for your analysis, consider disabling filtering and/or downsampling (e.g.
`lpfilt = FALSE` and/or `downsample = FALSE` in `glassbox()`).
! [2026-11-08 17:19:17] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
i [2026-11-08 17:19:19] [INFO] Epoching pupil data...
i [2026-11-08 17:19:19] [INFO] Block 1: found 3 matching events for PROBE
v [2026-11-08 17:19:19] [OKAY] Done!
v [2026-11-08 17:19:19] [OKAY] Block 1: pupil data from 3 unique event messages
extracted
v [2026-11-08 17:19:19] [OKAY] Pupil epoching completed in 0.09 seconds
i [2026-11-08 17:19:19] [INFO] Recalculating epoched confounds for new
epochs...
v [2026-11-08 17:19:19] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:19:19] [OKAY] Running eyeris::resample()
i [2026-11-08 17:19:19] [INFO] Processing block: block_1
v [2026-11-08 17:19:19] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:19:19] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:19:19] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:19:19] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:19:19] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:19:19] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:19:19] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:19:19] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:19:19] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:19:19] [INFO] Block processing summary:
i [2026-11-08 17:19:19] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:19:19] [OKAY] Running eyeris::summarize_confounds()
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:19:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:28] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
! [2026-11-08 17:19:40] [WARN] No detrend data found for run-01
processing file: sub-001_task-test.Rmd
output file: sub-001_task-test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS sub-001_task-test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001_task-test.html --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --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 /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --syntax-highlighting none --variable highlightjs=1 --variable theme=bootstrap --css /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /home/hornik/tmp/scratch/RtmpPJbS1W/rmarkdown-str1f24c54fb35ff.html
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
Output created: sub-001_task-test.html
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:19:44] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:19:44] [OKAY] Running eyeris::resample()
i [2026-11-08 17:19:44] [INFO] Processing block: block_1
v [2026-11-08 17:19:44] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:19:44] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:19:44] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:19:44] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:19:44] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:19:44] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:19:44] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:19:44] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:19:44] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:19:44] [INFO] Block processing summary:
i [2026-11-08 17:19:44] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:19:44] [OKAY] Running eyeris::summarize_confounds()
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:19:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:19:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
! [2026-11-08 17:20:06] [WARN] No detrend data found for run-01
processing file: sub-002_task-test.Rmd
output file: sub-002_task-test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS sub-002_task-test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002_task-test.html --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --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 /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --syntax-highlighting none --variable highlightjs=1 --variable theme=bootstrap --css /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /home/hornik/tmp/scratch/RtmpPJbS1W/rmarkdown-str1f24c57abab095.html
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
Output created: sub-002_task-test.html
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:20:09] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:20:09] [OKAY] Running eyeris::resample()
i [2026-11-08 17:20:09] [INFO] Processing block: block_1
v [2026-11-08 17:20:09] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:20:09] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:20:09] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:20:09] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:20:09] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:20:09] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:20:09] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:20:09] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:20:09] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:20:09] [INFO] Block processing summary:
i [2026-11-08 17:20:09] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:20:09] [OKAY] Running eyeris::summarize_confounds()
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:20:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:11] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
! [2026-11-08 17:20:29] [WARN] No detrend data found for run-01
processing file: sub-003_task-test.Rmd
output file: sub-003_task-test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS sub-003_task-test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003_task-test.html --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --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 /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --syntax-highlighting none --variable highlightjs=1 --variable theme=bootstrap --css /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /home/hornik/tmp/scratch/RtmpPJbS1W/rmarkdown-str1f24c54104d3ce.html
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
Output created: sub-003_task-test.html
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:20:32] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:20:32] [OKAY] Running eyeris::resample()
i [2026-11-08 17:20:32] [INFO] Processing block: block_1
v [2026-11-08 17:20:32] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:20:32] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:20:33] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:20:33] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:20:33] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:20:33] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:20:33] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:20:33] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:20:33] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:20:33] [INFO] Block processing summary:
i [2026-11-08 17:20:33] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:20:33] [OKAY] Running eyeris::summarize_confounds()
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:20:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
i [2026-11-08 17:20:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
possible blocks: 1
! [2026-11-08 17:20:53] [WARN] No detrend data found for run-01
processing file: sub-004_task-test.Rmd
output file: sub-004_task-test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS sub-004_task-test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004_task-test.html --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --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 /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --syntax-highlighting none --variable highlightjs=1 --variable theme=bootstrap --css /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /home/hornik/tmp/scratch/RtmpPJbS1W/rmarkdown-str1f24c512239078.html
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
Output created: sub-004_task-test.html
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:20:58] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:20:58] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_bids/derivatives/test-study.eyerisdb
i [2026-11-08 17:20:58] [INFO] Disconnected from eyeris database
Saving _problems/test-parquet-split-57.R
Saving _problems/test-parquet-split-79.R
Saving _problems/test-parquet-split-79.R
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:20:58] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:20:59] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_bids_read/derivatives/read-test.eyerisdb
i [2026-11-08 17:20:59] [INFO] Disconnected from eyeris database
Saving _problems/test-parquet-split-134.R
Saving _problems/test-parquet-split-143.R
Saving _problems/test-parquet-split-147.R
Saving _problems/test-parquet-split-150.R
Saving _problems/test-parquet-split-151.R
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:20:59] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:20:59] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_bids_size/derivatives/size-test.eyerisdb
i [2026-11-08 17:20:59] [INFO] Disconnected from eyeris database
Saving _problems/test-parquet-split-206.R
Saving _problems/test-parquet-split-207.R
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
i [2026-11-08 17:21:00] [INFO] Disconnected from eyeris database
duckdb keeps downloaded extensions and secrets in a temporary directory:
i /home/hornik/tmp/scratch/RtmpPJbS1W/duckdb
This is removed when the R session ends.
* Extensions are re-downloaded each session.
* Secrets are lost.
i Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
i Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
i See ?duckdb_storage for details and alternatives.
v [2026-11-08 17:21:00] [OKAY] Connected to eyeris database:
/home/hornik/tmp/scratch/RtmpPJbS1W/test_bids_empty/derivatives/empty-test.eyerisdb
! [2026-11-08 17:21:00] [WARN] No valid tables found in database (after
excluding temp tables)
i [2026-11-08 17:21:00] [INFO] Disconnected from eyeris database
Saving _problems/test-parquet-split-272.R
v [2026-11-08 17:21:01] [OKAY] Running eyeris::load_asc()
v [2026-11-08 17:21:01] [OKAY] Running eyeris::resample()
i [2026-11-08 17:21:01] [INFO] Processing block: block_1
v [2026-11-08 17:21:01] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:21:01] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:21:01] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:21:01] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
v [2026-11-08 17:21:01] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:21:01] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:21:01] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:21:01] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:21:01] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:21:01] [INFO] Block processing summary:
i [2026-11-08 17:21:01] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:21:01] [OKAY] Running eyeris::summarize_confounds()
v [2026-11-08 17:21:02] [OKAY] Running eyeris::load_asc()
i [2026-11-08 17:21:02] [INFO] Binocular data detected. Processing average
mode.
v [2026-11-08 17:21:02] [OKAY] Running eyeris::resample()
i [2026-11-08 17:21:02] [INFO] Processing block: block_1
v [2026-11-08 17:21:02] [OKAY] Running eyeris::deblink() for block_1
v [2026-11-08 17:21:02] [OKAY] Running eyeris::detransient() for block_1
v [2026-11-08 17:21:02] [OKAY] Running eyeris::interpolate() for block_1
! [2026-11-08 17:21:02] [WARN] Interpolation now leaves gaps longer than 250 ms
as `NA` instead of interpolating across them (following Kret & Sjak-Shie,
2018). This is a change in default behavior from eyeris <= 3.2.0 and may affect
your results. To restore the previous behavior, set `interpolate =
list(max_gap_ms = Inf)` in `glassbox()` (or `max_gap_ms = Inf` in
`interpolate()`).
! [2026-11-08 17:21:02] [WARN] No NAs detected in pupil data... Skipping
interpolation!
v [2026-11-08 17:21:02] [OKAY] Running eyeris::lpfilt() for block_1
! [2026-11-08 17:21:02] [WARN] Skipping eyeris::downsample() for block_1
! [2026-11-08 17:21:02] [WARN] Skipping eyeris::bin() for block_1
! [2026-11-08 17:21:02] [WARN] Skipping eyeris::detrend() for block_1
v [2026-11-08 17:21:02] [OKAY] Running eyeris::zscore() for block_1
i [2026-11-08 17:21:02] [INFO] Block processing summary:
i [2026-11-08 17:21:02] [INFO] block_1: OK (steps: 6, latest:
pupil_raw_deblink_detransient_interpolate_lpfilt_z)
v [2026-11-08 17:21:02] [OKAY] Running eyeris::summarize_confounds()
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected: 1 of 4
intervals (25%) differ from the expected 1 ms spacing (nominal rate: 1000 Hz);
1 longer and 0 shorter. Estimated 2 dropped sample(s); largest long interval is
3 ms (~3x expected). First irregular interval occurs before sample 4. This
violates the uniform-sampling assumption of the eyeris pipeline. Consider
resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected: 2 of 7
intervals (28.57%) differ from the expected 1 ms spacing (nominal rate: 1000
Hz); 2 longer and 0 shorter. Estimated 5 dropped sample(s); largest long
interval is 4 ms (~4x expected). First irregular interval occurs before sample
4. This violates the uniform-sampling assumption of the eyeris pipeline.
Consider resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected: 2 of 5
intervals (40%) differ from the expected 4 ms spacing (nominal rate: 250 Hz); 0
longer and 2 shorter. First irregular interval occurs before sample 3. This
violates the uniform-sampling assumption of the eyeris pipeline. Consider
resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected: 1 of 4
intervals (25%) differ from the expected 1 ms spacing (nominal rate: inferred
from data); 1 longer and 0 shorter. Estimated 2 dropped sample(s); largest long
interval is 3 ms (~3x expected). First irregular interval occurs before sample
4. This violates the uniform-sampling assumption of the eyeris pipeline.
Consider resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected: 1 of 6
intervals (16.67%) differ from the expected 1 ms spacing (nominal rate: 1000
Hz); 1 longer and 0 shorter. Estimated 996 dropped sample(s); largest long
interval is 997 ms (~997x expected). First irregular interval occurs before
sample 5. This violates the uniform-sampling assumption of the eyeris pipeline.
Consider resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected in
block_2: 1 of 2 intervals (50%) differ from the expected 1 ms spacing (nominal
rate: 1000 Hz); 1 longer and 0 shorter. Estimated 2 dropped sample(s); largest
long interval is 3 ms (~3x expected). First irregular interval occurs before
sample 3. This violates the uniform-sampling assumption of the eyeris pipeline.
Consider resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Non-uniform sampling intervals detected: 1 of 4
intervals (25%) differ from the expected 1 ms spacing (nominal rate: 1000 Hz);
1 longer and 0 shorter. Estimated 1 dropped sample(s); largest long interval is
2 ms (~2x expected). First irregular interval occurs before sample 3. This
violates the uniform-sampling assumption of the eyeris pipeline. Consider
resampling onto a regular time grid before preprocessing.
! [2026-11-08 17:21:13] [WARN] Effective sampling rate (~500 Hz, 2 ms spacing)
is lower than the device's reported 1000 Hz (1 ms). This can indicate
systematic sample dropout (e.g., every Nth sample missing), which leaves a
uniform but coarser time grid that the eyeris pipeline would otherwise treat as
the true sampling rate. Verify the recording against the tracker's configured
sampling rate.
[ FAIL 12 | WARN 1 | SKIP 5 | PASS 717 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test-bidsify-multirun-epochs.R:87:3',
'test-bidsify-multirun-epochs.R:125:3',
'test-bidsify-runnum-override.R:58:3',
'test-bidsify-runnum-override.R:105:3',
'test-bidsify-task-run-collision.R:46:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-chunked-processing.R:200:5'): chunked processing works with parquet output ──
Error in `parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))`: Cannot call parquet___arrow___ArrowReaderProperties__Make(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─arrow::read_parquet(parquet_file) at test-chunked-processing.R:200:5
2. ├─ParquetFileReader$create(file, props = props, mmap = mmap, ...)
3. │ └─arrow:::assert_is(props, "ParquetArrowReaderProperties")
4. │ ├─assertthat::assert_that(inherits(object, class), msg = msg)
5. │ │ └─assertthat::see_if(..., env = env, msg = msg)
6. │ │ ├─base::tryCatch(...)
7. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
10. │ │ └─base::eval(assertion, env)
11. │ │ └─base::eval(assertion, env)
12. │ └─base::inherits(object, class)
13. └─ParquetArrowReaderProperties$create()
14. └─arrow:::parquet___arrow___ArrowReaderProperties__Make(isTRUE(use_threads))
── Failure ('test-parquet-split.R:57:3'): eyeris_db_to_parquet creates correctly named files and folders ──
Expected `length(result$files)` to equal 2.
Differences:
`actual`: 0.0
`expected`: 2.0
── Failure ('test-parquet-split.R:79:5'): eyeris_db_to_parquet creates correctly named files and folders ──
Expected `expected_filepath %in% result$files` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-parquet-split.R:79:5'): eyeris_db_to_parquet creates correctly named files and folders ──
Expected `expected_filepath %in% result$files` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-parquet-split.R:134:3'): read_eyeris_parquet correctly reads back split data ──
Expected `length(split_result$files)` to equal 2.
Differences:
`actual`: 0.0
`expected`: 2.0
── Failure ('test-parquet-split.R:143:3'): read_eyeris_parquet correctly reads back split data ──
Expected `nrow(read_data)` to equal `nrow(original_data)`.
Differences:
`actual`: 0
`expected`: 50
── Failure ('test-parquet-split.R:144:3'): read_eyeris_parquet correctly reads back split data ──
Expected `all(...)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-parquet-split.R:150:3'): read_eyeris_parquet correctly reads back split data ──
Expected `sort(read_data$time)` to equal `sort(original_data$time)`.
Differences:
`actual` is NULL
`expected` is an integer vector (1, 2, 3, 4, 5, ...)
── Failure ('test-parquet-split.R:151:3'): read_eyeris_parquet correctly reads back split data ──
Expected `sort(read_data$pupil_left)` to equal `sort(original_data$pupil_left)`.
Differences:
`actual` is NULL
`expected` is an integer vector (1, 2, 3, 4, 5, ...)
── Failure ('test-parquet-split.R:206:3'): eyeris_db_to_parquet handles file size constraints ──
Expected `length(result$files) >= 2` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-parquet-split.R:207:3'): eyeris_db_to_parquet handles file size constraints ──
Expected `result$n_files_created >= 2` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Error ('test-parquet-split.R:269:5'): read_eyeris_parquet works with db_name parameter ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─arrow::write_parquet(test_data_1, file.path(db_folder, "my-study_timeseries_part-01-of-02.parquet")) at test-parquet-split.R:269:5
2. ├─ParquetFileWriter$create(...)
3. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
4. └─ParquetWriterProperties$create(...)
5. └─arrow:::parquet___WriterProperties___Builder__create()
[ FAIL 12 | WARN 1 | SKIP 5 | PASS 717 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc