R Under development (unstable) (2026-03-15 r89634 ucrt) -- "Unsuffered Consequences"
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> # 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(immundata)
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: duckplyr
The duckplyr package is configured to fall back to dplyr when it encounters an
incompatibility. Fallback events can be collected and uploaded for analysis to
guide future development. By default, data will be collected but no data will
be uploaded.
ℹ Automatic fallback uploading is not controlled and therefore disabled, see
  `?duckplyr::fallback()`.
✔ Number of reports ready for upload: 12.
→ Review with `duckplyr::fallback_review()`, upload with
  `duckplyr::fallback_upload()`.
ℹ Configure automatic uploading with `duckplyr::fallback_config()`.
✔ Overwriting dplyr methods with duckplyr methods.
ℹ Turn off with `duckplyr::methods_restore()`.
Loading immundata version 0.0.6
> 
> test_check("immundata")
Starting 2 test processes.
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 

> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Reading repertoire data 

> test-annotate-barcodes.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-barcodes.R:   2.
> test-annotate-barcodes.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-annotate-barcodes.R: i Checking if all files are of the same type

> test-annotate-barcodes.R: v All files have the same extension
> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 
> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Renaming the columns and schemas 

> test-annotate-barcodes.R: v Renaming is finished
> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Preprocessing the data 

> test-annotate-barcodes.R:   1. exclude_columns
> test-annotate-barcodes.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-barcodes.R: v Preprocessing plan is ready
> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Aggregating the data to receptors 

> test-annotate-barcodes.R: i No locus information found
> test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Postprocessing the data 

> test-annotate-barcodes.R:   1. prefix_barcodes
> test-annotate-barcodes.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-barcodes.R: v Postprocessing plan is ready
> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk 
> test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681d1963ce/annotations.parquet]
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483b363d77/annotations.parquet]
> test-annotate-barcodes.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681d1963ce/metadata.json]
> test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681d1963ce]
> test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681d1963ce']
> test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681d1963ce']
> test-annotate-barcodes.R: 
> test-annotate-barcodes.R: -- Summary 

> test-annotate-barcodes.R: i Time elapsed: 3.23 secs
> test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483b363d77/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483b363d77]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483b363d77']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483b363d77']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.78 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-annotate-external.R: 
> test-annotate-external.R: -- Reading repertoire data 

> test-annotate-external.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R: v Postprocessing plan is ready
> test-annotate-external.R:   2.
> test-annotate-external.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-annotate-external.R: i Checking if all files are of the same type
> test-annotate-external.R: v All files have the same extension
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4810a820c1/annotations.parquet]
> test-annotate-external.R: 
> test-annotate-external.R: -- Renaming the columns and schemas 
> test-annotate-external.R: v Renaming is finished
> test-annotate-external.R: 
> test-annotate-external.R: -- Preprocessing the data 

> test-annotate-external.R:   1. exclude_columns
> test-annotate-external.R:   2. filter_nonproductive
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4810a820c1/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4810a820c1]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4810a820c1']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4810a820c1']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.79 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-external.R: v Preprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Aggregating the data to receptors 
> test-annotate-external.R: i No locus information found
> test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Postprocessing the data 

> test-annotate-external.R:   1. prefix_barcodes
> test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-external.R: v Postprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Saving the newly created ImmunData to disk 
> test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6852fb7e87/annotations.parquet]
> test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6852fb7e87/metadata.json]
> test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6852fb7e87]
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6852fb7e87']
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6852fb7e87']
> test-annotate-external.R: 
> test-annotate-external.R: -- Summary 

> test-annotate-external.R: i Time elapsed: 3.14 secs
> test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-annotate-external.R: 
> test-annotate-external.R: -- Reading repertoire data 

> test-annotate-external.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-external.R:   2.
> test-annotate-external.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-annotate-external.R: i Checking if all files are of the same type
> test-annotate-external.R: v All files have the same extension
> test-annotate-external.R: 
> test-annotate-external.R: -- Renaming the columns and schemas 

> test-annotate-external.R: v Renaming is finished
> test-annotate-external.R: 
> test-annotate-external.R: -- Preprocessing the data 

> test-annotate-external.R:   1. exclude_columns
> test-annotate-external.R:   2. filter_nonproductive
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 
> test-agg-strata.R:   1. prefix_barcodes
> test-annotate-external.R: v Preprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Aggregating the data to receptors 

> test-annotate-external.R: i No locus information found
> test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4859b921d7/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4859b921d7/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4859b921d7]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4859b921d7']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4859b921d7']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 
> test-agg-strata.R: i Time elapsed: 3.88 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Postprocessing the data 

> test-annotate-external.R:   1. prefix_barcodes
> test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-external.R: v Postprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Saving the newly created ImmunData to disk 
> test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6825554e67/annotations.parquet]
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6825554e67/metadata.json]
> test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6825554e67]
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6825554e67']
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6825554e67']
> test-annotate-external.R: 
> test-annotate-external.R: -- Summary 

> test-annotate-external.R: i Time elapsed: 3.03 secs
> test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-external.R: 
> test-annotate-external.R: -- Reading repertoire data 
> test-annotate-external.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-external.R:   2.
> test-annotate-external.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-annotate-external.R: i Checking if all files are of the same type
> test-annotate-external.R: v All files have the same extension
> test-annotate-external.R: 
> test-annotate-external.R: -- Renaming the columns and schemas 

> test-annotate-external.R: v Renaming is finished
> test-annotate-external.R: 
> test-annotate-external.R: -- Preprocessing the data 
> test-annotate-external.R:   1. exclude_columns
> test-annotate-external.R:   2. filter_nonproductive
> test-annotate-external.R: v Preprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Aggregating the data to receptors 

> test-annotate-external.R: i No locus information found
> test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481b4c4795/annotations.parquet]
> test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Postprocessing the data 
> test-annotate-external.R:   1. prefix_barcodes
> test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-external.R: v Postprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Saving the newly created ImmunData to disk 
> test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68695e2ecc/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481b4c4795/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481b4c4795]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481b4c4795']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481b4c4795']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 
> test-agg-strata.R: i Time elapsed: 3.87 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68695e2ecc/metadata.json]
> test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68695e2ecc]
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68695e2ecc']
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68695e2ecc']
> test-annotate-external.R: 
> test-annotate-external.R: -- Summary 
> test-annotate-external.R: i Time elapsed: 2.99 secs
> test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-external.R: 
> test-annotate-external.R: -- Reading repertoire data 
> test-annotate-external.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-external.R:   2.
> test-annotate-external.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-annotate-external.R: i Checking if all files are of the same type
> test-annotate-external.R: v All files have the same extension
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-annotate-external.R: 
> test-annotate-external.R: -- Renaming the columns and schemas 
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 
> test-annotate-external.R: v Renaming is finished
> test-annotate-external.R: 
> test-annotate-external.R: -- Preprocessing the data 
> test-annotate-external.R:   1. exclude_columns
> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-annotate-external.R:   2. filter_nonproductive
> test-agg-strata.R:   2. filter_nonproductive
> test-annotate-external.R: v Preprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Aggregating the data to receptors 

> test-annotate-external.R: i No locus information found
> test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Postprocessing the data 

> test-annotate-external.R:   1. prefix_barcodes
> test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-external.R: v Postprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Saving the newly created ImmunData to disk 
> test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e682c412f5/annotations.parquet]
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e682c412f5/metadata.json]
> test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e682c412f5]
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e682c412f5']
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e682c412f5']
> test-annotate-external.R: 
> test-annotate-external.R: -- Summary 

> test-annotate-external.R: i Time elapsed: 2.99 secs
> test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-external.R: 
> test-annotate-external.R: -- Reading repertoire data 
> test-annotate-external.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-external.R:   2.
> test-annotate-external.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-annotate-external.R: i Checking if all files are of the same type
> test-annotate-external.R: v All files have the same extension
> test-annotate-external.R: 
> test-annotate-external.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-annotate-external.R: v Renaming is finished
> test-annotate-external.R: 
> test-annotate-external.R: -- Preprocessing the data 
> test-annotate-external.R:   1. exclude_columns
> test-agg-strata.R:   1. prefix_barcodes
> test-annotate-external.R:   2. filter_nonproductive
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481eea5039/annotations.parquet]
> test-annotate-external.R: v Preprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Aggregating the data to receptors 

> test-annotate-external.R: i No locus information found
> test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481eea5039/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481eea5039]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481eea5039']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481eea5039']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.84 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Postprocessing the data 

> test-annotate-external.R:   1. prefix_barcodes
> test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-external.R: v Postprocessing plan is ready
> test-annotate-external.R: 
> test-annotate-external.R: -- Saving the newly created ImmunData to disk 
> test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68152fb41/annotations.parquet]
> test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68152fb41/metadata.json]
> test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68152fb41]
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68152fb41']
> test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68152fb41']
> test-annotate-external.R: 
> test-annotate-external.R: -- Summary 
> test-annotate-external.R: i Time elapsed: 2.99 secs
> test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Reading repertoire data 

> test-annotate-receptors.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-receptors.R:   2.
> test-annotate-receptors.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-annotate-receptors.R: i Checking if all files are of the same type
> test-annotate-receptors.R: v All files have the same extension
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Renaming the columns and schemas 

> test-annotate-receptors.R: v Renaming is finished
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Preprocessing the data 

> test-annotate-receptors.R:   1. exclude_columns
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-annotate-receptors.R:   2. filter_nonproductive
> test-annotate-receptors.R: v Preprocessing plan is ready
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Aggregating the data to receptors 
> test-annotate-receptors.R: i No locus information found
> test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48269d21d0/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48269d21d0/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48269d21d0]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48269d21d0']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48269d21d0']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.81 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Postprocessing the data 

> test-annotate-receptors.R:   1. prefix_barcodes
> test-annotate-receptors.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-receptors.R: v Postprocessing plan is ready
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Saving the newly created ImmunData to disk 
> test-annotate-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c7627b3/annotations.parquet]
> test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c7627b3/metadata.json]
> test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c7627b3]
> test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c7627b3']
> test-agg-strata.R: Rows: 2 Columns: 4
> test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c7627b3']
> test-annotate-receptors.R: 
> test-annotate-receptors.R: -- Summary 
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-annotate-receptors.R: i Time elapsed: 3.11 secs
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 

> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-compute-collect-immundata.R: Rows: 2 Columns: 4
> test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
> test-compute-collect-immundata.R: Delimiter: "\t"
> test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-compute-collect-immundata.R: v Metadata parsed successfully
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Reading repertoire data 
> test-compute-collect-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-compute-collect-immundata.R:   2.
> test-compute-collect-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-compute-collect-immundata.R: i Checking if all files are of the same type
> test-compute-collect-immundata.R: v All files have the same extension
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Renaming the columns and schemas 

> test-compute-collect-immundata.R: v Renaming is finished
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Preprocessing the data 
> test-compute-collect-immundata.R:   1. exclude_columns
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-compute-collect-immundata.R:   2. filter_nonproductive
> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-compute-collect-immundata.R: v Preprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Aggregating the data to receptors 

> test-compute-collect-immundata.R: i No locus information found
> test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4858c53689/annotations.parquet]
> test-compute-collect-immundata.R: v Joining plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Postprocessing the data 
> test-compute-collect-immundata.R:   1. prefix_barcodes
> test-compute-collect-immundata.R: v Postprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk 

> test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c25675b/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4858c53689/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4858c53689]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4858c53689']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4858c53689']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.91 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c25675b/metadata.json]
> test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c25675b]
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c25675b']
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684c25675b']
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Summary 
> test-compute-collect-immundata.R: i Time elapsed: 3.84 secs
> test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-compute-collect-immundata.R: Rows: 2 Columns: 4
> test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
> test-compute-collect-immundata.R: Delimiter: "\t"
> test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-compute-collect-immundata.R: v Metadata parsed successfully
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Reading repertoire data 
> test-compute-collect-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-compute-collect-immundata.R:   2.
> test-compute-collect-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-compute-collect-immundata.R: i Checking if all files are of the same type
> test-compute-collect-immundata.R: v All files have the same extension
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Renaming the columns and schemas 

> test-compute-collect-immundata.R: v Renaming is finished
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Preprocessing the data 
> test-compute-collect-immundata.R:   1. exclude_columns
> test-compute-collect-immundata.R:   2. filter_nonproductive
> test-compute-collect-immundata.R: v Preprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Aggregating the data to receptors 

> test-compute-collect-immundata.R: i No locus information found
> test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-compute-collect-immundata.R: v Joining plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Postprocessing the data 

> test-compute-collect-immundata.R:   1. prefix_barcodes
> test-compute-collect-immundata.R: v Postprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk 

> test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681527e9a/annotations.parquet]
> test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681527e9a/metadata.json]
> test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681527e9a]
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681527e9a']
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e681527e9a']
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Summary 
> test-compute-collect-immundata.R: i Time elapsed: 3.94 secs
> test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-compute-collect-immundata.R: Rows: 2 Columns: 4
> test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
> test-compute-collect-immundata.R: Delimiter: "\t"
> test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-compute-collect-immundata.R: v Metadata parsed successfully
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Reading repertoire data 
> test-compute-collect-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-compute-collect-immundata.R:   2.
> test-compute-collect-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-compute-collect-immundata.R: i Checking if all files are of the same type
> test-compute-collect-immundata.R: v All files have the same extension
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Renaming the columns and schemas 
> test-compute-collect-immundata.R: v Renaming is finished
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Preprocessing the data 

> test-compute-collect-immundata.R:   1. exclude_columns
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-compute-collect-immundata.R:   2. filter_nonproductive
> test-compute-collect-immundata.R: v Preprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Aggregating the data to receptors 

> test-compute-collect-immundata.R: i No locus information found
> test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4834094d1f/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4834094d1f/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4834094d1f]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4834094d1f']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4834094d1f']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.96 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-compute-collect-immundata.R: v Joining plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Postprocessing the data 

> test-compute-collect-immundata.R:   1. prefix_barcodes
> test-compute-collect-immundata.R: v Postprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk 

> test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6847d36299/annotations.parquet]
> test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6847d36299/metadata.json]
> test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6847d36299]
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6847d36299']
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6847d36299']
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Summary 

> test-compute-collect-immundata.R: i Time elapsed: 3.91 secs
> test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-compute-collect-immundata.R: Rows: 2 Columns: 4
> test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
> test-compute-collect-immundata.R: Delimiter: "\t"
> test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-compute-collect-immundata.R: v Metadata parsed successfully
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Reading repertoire data 
> test-compute-collect-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-compute-collect-immundata.R:   2.
> test-compute-collect-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-compute-collect-immundata.R: i Checking if all files are of the same type
> test-compute-collect-immundata.R: v All files have the same extension
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Renaming the columns and schemas 

> test-compute-collect-immundata.R: v Renaming is finished
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Preprocessing the data 

> test-compute-collect-immundata.R:   1. exclude_columns
> test-compute-collect-immundata.R:   2. filter_nonproductive
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-compute-collect-immundata.R: v Preprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Aggregating the data to receptors 
> test-compute-collect-immundata.R: i No locus information found
> test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483d9259d3/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483d9259d3/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483d9259d3]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483d9259d3']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a483d9259d3']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.82 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 
> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-compute-collect-immundata.R: v Joining plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Postprocessing the data 

> test-compute-collect-immundata.R:   1. prefix_barcodes
> test-compute-collect-immundata.R: v Postprocessing plan is ready
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk 

> test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6867554024/annotations.parquet]
> test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6867554024/metadata.json]
> test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6867554024]
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6867554024']
> test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6867554024']
> test-compute-collect-immundata.R: 
> test-compute-collect-immundata.R: -- Summary 

> test-compute-collect-immundata.R: i Time elapsed: 3.84 secs
> test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Reading repertoire data 

> test-filter-barcodes.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-barcodes.R:   2.
> test-filter-barcodes.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-barcodes.R: i Checking if all files are of the same type
> test-filter-barcodes.R: v All files have the same extension
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Renaming the columns and schemas 

> test-filter-barcodes.R: v Renaming is finished
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Preprocessing the data 

> test-filter-barcodes.R:   1. exclude_columns
> test-filter-barcodes.R:   2. filter_nonproductive
> test-filter-barcodes.R: v Preprocessing plan is ready
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Aggregating the data to receptors 

> test-filter-barcodes.R: i No locus information found
> test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d6c6c5/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d6c6c5/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d6c6c5]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d6c6c5']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d6c6c5']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 4.01 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Postprocessing the data 
> test-filter-barcodes.R:   1. prefix_barcodes
> test-filter-barcodes.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-barcodes.R: v Postprocessing plan is ready
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Saving the newly created ImmunData to disk 
> test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848be28b0/annotations.parquet]
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848be28b0/metadata.json]
> test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848be28b0]
> test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848be28b0']
> test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848be28b0']
> test-filter-barcodes.R: 
> test-filter-barcodes.R: -- Summary 
> test-filter-barcodes.R: i Time elapsed: 3.07 secs
> test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R:   2. filter_nonproductive
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Reading repertoire data 

> test-filter-immundata-exact.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-exact.R:   2.
> test-filter-immundata-exact.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata-exact.R: i Checking if all files are of the same type
> test-filter-immundata-exact.R: v All files have the same extension
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Renaming the columns and schemas 

> test-filter-immundata-exact.R: v Renaming is finished
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Preprocessing the data 

> test-filter-immundata-exact.R:   1. exclude_columns
> test-filter-immundata-exact.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-exact.R: v Preprocessing plan is ready
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Aggregating the data to receptors 

> test-filter-immundata-exact.R: i No locus information found
> test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Postprocessing the data 

> test-filter-immundata-exact.R:   1. prefix_barcodes
> test-filter-immundata-exact.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6872e26d1/annotations.parquet]
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6872e26d1/metadata.json]
> test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6872e26d1]
> test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6872e26d1']
> test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6872e26d1']
> test-filter-immundata-exact.R: 
> test-filter-immundata-exact.R: -- Summary 

> test-filter-immundata-exact.R: i Time elapsed: 2.93 secs
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48220758e7/annotations.parquet]
> test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48220758e7/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48220758e7]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48220758e7']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48220758e7']
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Reading repertoire data 
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 
> test-filter-immundata-hamm.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-hamm.R:   2.
> test-filter-immundata-hamm.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Time elapsed: 3.82 secs
> test-filter-immundata-hamm.R: i Checking if all files are of the same type
> test-filter-immundata-hamm.R: v All files have the same extension
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Renaming the columns and schemas 

> test-filter-immundata-hamm.R: v Renaming is finished
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Preprocessing the data 

> test-filter-immundata-hamm.R:   1. exclude_columns
> test-filter-immundata-hamm.R:   2. filter_nonproductive
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-filter-immundata-hamm.R: v Preprocessing plan is ready
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Aggregating the data to receptors 
> test-filter-immundata-hamm.R: i No locus information found
> test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 
> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Postprocessing the data 

> test-filter-immundata-hamm.R:   1. prefix_barcodes
> test-filter-immundata-hamm.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-hamm.R: v Postprocessing plan is ready
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685daa424f/annotations.parquet]
> test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685daa424f/metadata.json]
> test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685daa424f]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685daa424f']
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685daa424f']
> test-filter-immundata-hamm.R: 
> test-filter-immundata-hamm.R: -- Summary 
> test-filter-immundata-hamm.R: i Time elapsed: 2.96 secs
> test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Reading repertoire data 

> test-filter-immundata-lev.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-lev.R:   2.
> test-filter-immundata-lev.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Renaming the columns and schemas 

> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Preprocessing the data 

> test-filter-immundata-lev.R:   1. exclude_columns
> test-filter-immundata-lev.R:   2. filter_nonproductive
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-filter-immundata-lev.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Aggregating the data to receptors 

> test-filter-immundata-lev.R: i No locus information found
> test-agg-strata.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 
> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a482c8d76f6/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a482c8d76f6/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a482c8d76f6]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a482c8d76f6']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a482c8d76f6']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.86 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-agg-strata.R: Rows: 2 Columns: 4
> test-agg-strata.R: -- Column specification --------------------------------------------------------
> test-agg-strata.R: Delimiter: "\t"
> test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
> test-agg-strata.R: 
> test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-agg-strata.R: v Metadata parsed successfully
> test-agg-strata.R: 
> test-agg-strata.R: -- Reading repertoire data 
> test-agg-strata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-agg-strata.R:   2.
> test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-agg-strata.R: i Checking if all files are of the same type
> test-agg-strata.R: v All files have the same extension
> test-agg-strata.R: 
> test-agg-strata.R: -- Renaming the columns and schemas 

> test-agg-strata.R: v Renaming is finished
> test-agg-strata.R: 
> test-agg-strata.R: -- Preprocessing the data 

> test-agg-strata.R:   1. exclude_columns
> test-agg-strata.R:   2. filter_nonproductive
> test-agg-strata.R: v Preprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Aggregating the data to receptors 

> test-agg-strata.R: i No locus information found
> test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Postprocessing the data 

> test-filter-immundata-lev.R:   1. prefix_barcodes
> test-filter-immundata-lev.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-lev.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68408e64f9/annotations.parquet]
> test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68408e64f9/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68408e64f9]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68408e64f9']
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68408e64f9']
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Summary 

> test-filter-immundata-lev.R: i Time elapsed: 2.98 secs
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Reading repertoire data 
> test-filter-immundata-lev.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-lev.R:   2.
> test-filter-immundata-lev.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Renaming the columns and schemas 

> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Preprocessing the data 

> test-filter-immundata-lev.R:   1. exclude_columns
> test-filter-immundata-lev.R:   2. filter_nonproductive
> test-filter-immundata-lev.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Aggregating the data to receptors 

> test-filter-immundata-lev.R: i No locus information found
> test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-agg-strata.R: v Joining plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Postprocessing the data 

> test-agg-strata.R:   1. prefix_barcodes
> test-agg-strata.R: v Postprocessing plan is ready
> test-agg-strata.R: 
> test-agg-strata.R: -- Saving the newly created ImmunData to disk 

> test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481c39ad3/annotations.parquet]
> test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481c39ad3/metadata.json]
> test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481c39ad3]
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481c39ad3']
> test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481c39ad3']
> test-agg-strata.R: 
> test-agg-strata.R: -- Summary 

> test-agg-strata.R: i Time elapsed: 3.78 secs
> test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Postprocessing the data 
> test-filter-immundata-lev.R:   1. prefix_barcodes
> test-filter-immundata-lev.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-lev.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685d17123c/annotations.parquet]
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Reading repertoire data 

> test-filter-immundata-regex.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-regex.R:   2.
> test-filter-immundata-regex.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Renaming the columns and schemas 

> test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685d17123c/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685d17123c]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685d17123c']
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685d17123c']
> test-filter-immundata-lev.R: 
> test-filter-immundata-lev.R: -- Summary 
> test-filter-immundata-lev.R: i Time elapsed: 3.06 secs
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Preprocessing the data 
> test-filter-immundata-regex.R:   1. exclude_columns
> test-filter-immundata-regex.R:   2. filter_nonproductive
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R: 
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Reading repertoire data 
> test-filter-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata.R:   2.
> test-filter-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Renaming the columns and schemas 

> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Preprocessing the data 

> test-filter-immundata.R:   1. exclude_columns
> test-filter-immundata-regex.R: v Preprocessing plan is ready
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Aggregating the data to receptors 

> test-filter-immundata-regex.R: i No locus information found
> test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R:   2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Aggregating the data to receptors 

> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Postprocessing the data 

> test-filter-immundata-regex.R:   1. prefix_barcodes
> test-filter-immundata-regex.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-regex.R: v Postprocessing plan is ready
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4838c213ed/annotations.parquet]
> test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4838c213ed/metadata.json]
> test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4838c213ed]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4838c213ed']
> test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4838c213ed']
> test-filter-immundata-regex.R: 
> test-filter-immundata-regex.R: -- Summary 

> test-filter-immundata-regex.R: i Time elapsed: 2.95 secs
> test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Reading repertoire data 

> test-filter-receptors.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-receptors.R:   2.
> test-filter-receptors.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Renaming the columns and schemas 

> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Preprocessing the data 

> test-filter-receptors.R:   1. exclude_columns
> test-filter-receptors.R:   2. filter_nonproductive
> test-filter-immundata.R: v Joining plan is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Postprocessing the data 

> test-filter-immundata.R:   1. prefix_barcodes
> test-filter-immundata.R: v Postprocessing plan is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848b43162/annotations.parquet]
> test-filter-receptors.R: v Preprocessing plan is ready
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Aggregating the data to receptors 

> test-filter-receptors.R: i No locus information found
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848b43162/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848b43162]
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848b43162']
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6848b43162']
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Summary 
> test-filter-immundata.R: i Time elapsed: 3.85 secs
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Reading repertoire data 
> test-filter-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata.R:   2.
> test-filter-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Renaming the columns and schemas 

> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Preprocessing the data 

> test-filter-immundata.R:   1. exclude_columns
> test-filter-immundata.R:   2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Aggregating the data to receptors 

> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Postprocessing the data 

> test-filter-receptors.R:   1. prefix_barcodes
> test-filter-receptors.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-receptors.R: v Postprocessing plan is ready
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Saving the newly created ImmunData to disk 
> test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a487a01f32/annotations.parquet]
> test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a487a01f32/metadata.json]
> test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a487a01f32]
> test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a487a01f32']
> test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a487a01f32']
> test-filter-receptors.R: 
> test-filter-receptors.R: -- Summary 

> test-filter-receptors.R: i Time elapsed: 3.05 secs
> test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 

> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible

> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Postprocessing the data 

> test-filter-immundata.R:   1. prefix_barcodes
> test-filter-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata.R: v Postprocessing plan is ready
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
> test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685514346/annotations.parquet]
> test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685514346/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685514346]
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685514346']
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e685514346']
> test-filter-immundata.R: 
> test-filter-immundata.R: -- Summary 

> test-filter-immundata.R: i Time elapsed: 3.03 secs
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-io-repertoires-agg-stepwise.R: 
> test-io-repertoires-agg-stepwise.R: -- Reading repertoire data 

> test-io-repertoires-agg-stepwise.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e683bba106e.tsv
> test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type
> test-io-repertoires-agg-stepwise.R: v All files have the same extension
> test-io-repertoires-agg-stepwise.R: 
> test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors 
> test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\legacy_v1_6a4856bf4361/annotations.parquet]
> test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg-stepwise.R: 
> test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822df1cfe/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\legacy_v1_6a4856bf4361/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\legacy_v1_6a4856bf4361]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\legacy_v1_6a4856bf4361']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\legacy_v1_6a4856bf4361']
> test-io-repertoires-agg-stepwise.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822df1cfe/metadata.json]
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822df1cfe]
> test-io-immundata.R: i Time elapsed: 1.38 secs
> test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822df1cfe']
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822df1cfe']
> test-io-repertoires-agg-stepwise.R: 
> test-io-repertoires-agg-stepwise.R: -- Summary 

> test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.33 secs
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\legacy_v1_6a4856bf4361']
> test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Reading repertoire data 

> test-io-repertoires-agg.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6829393c73.tsv
> test-io-repertoires-agg.R: i Checking if all files are of the same type
> test-io-repertoires-agg.R: v All files have the same extension
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Aggregating the data to receptors 

> test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e687a56538c/annotations.parquet]
> test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e687a56538c/metadata.json]
> test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e687a56538c]
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e687a56538c']
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e687a56538c']
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Summary 
> test-io-repertoires-agg.R: i Time elapsed: 0.34 secs
> test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 

> test-io-immundata.R: i Time elapsed: 1.51 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Reading repertoire data 
> test-io-repertoires-agg.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6876d4c59.tsv
> test-io-repertoires-agg.R: i Checking if all files are of the same type
> test-io-repertoires-agg.R: v All files have the same extension
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Aggregating the data to receptors 
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68513410d7/annotations.parquet]
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 1.4 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68513410d7/metadata.json]
> test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68513410d7]
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68513410d7']
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68513410d7']
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Summary 
> test-io-repertoires-agg.R: i Time elapsed: 1.59 secs
> test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Reading repertoire data 
> test-io-repertoires-agg.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e682a4d4b50.tsv
> test-io-repertoires-agg.R: i Checking if all files are of the same type
> test-io-repertoires-agg.R: v All files have the same extension
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Aggregating the data to receptors 

> test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 1.4 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: Rows: 2 Columns: 4
> test-io-immundata.R: -- Column specification --------------------------------------------------------
> test-io-immundata.R: Delimiter: "\t"
> test-io-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-io-immundata.R: 
> test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-immundata.R: v Metadata parsed successfully
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R:   2.
> test-io-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864f2df5/annotations.parquet]
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864f2df5/metadata.json]
> test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864f2df5]
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864f2df5']
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864f2df5']
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Summary 
> test-io-repertoires-agg.R: i Time elapsed: 1.61 secs
> test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Reading repertoire data 
> test-io-repertoires-agg.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68228b2b0a.tsv
> test-io-repertoires-agg.R: i Checking if all files are of the same type
> test-io-repertoires-agg.R: v All files have the same extension
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Aggregating the data to receptors 

> test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6823d97405/annotations.parquet]
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-io-immundata.R: v Joining plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6823d97405/metadata.json]
> test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6823d97405]
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6823d97405']
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6823d97405']
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Summary 
> test-io-repertoires-agg.R: i Time elapsed: 2.08 secs
> test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 3.23 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Reading repertoire data 
> test-io-repertoires-agg.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6863674a47.tsv
> test-io-repertoires-agg.R: i Checking if all files are of the same type
> test-io-repertoires-agg.R: v All files have the same extension
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Aggregating the data to receptors 
> test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681d5b76b3/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 1.37 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001']
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002']
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681d5b76b3/metadata.json]
> test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681d5b76b3]
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681d5b76b3']
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681d5b76b3']
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Summary 
> test-io-repertoires-agg.R: i Time elapsed: 1.64 secs
> test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Reading repertoire data 
> test-io-repertoires-agg.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68280d13.tsv
> test-io-repertoires-agg.R: i Checking if all files are of the same type
> test-io-repertoires-agg.R: v All files have the same extension
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Renaming the columns and schemas 
> test-io-repertoires-agg.R: v Renaming is finished
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Preprocessing the data 
> test-io-repertoires-agg.R:   1. exclude_columns
> test-io-repertoires-agg.R:   2. filter_nonproductive
> test-io-repertoires-agg.R:   ! No columns with the productive specification found; skipping the filtering
> test-io-repertoires-agg.R: v Preprocessing plan is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Aggregating the data to receptors 
> test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 

> test-io-immundata.R: i Time elapsed: 1.45 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/snapshots/baseline/v001']
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")]
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002']
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\treated\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\treated\v001']
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB/annotations.parquet]
> test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Postprocessing the data 
> test-io-repertoires-agg.R:   1. prefix_barcodes
> test-io-repertoires-agg.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-agg.R: v Postprocessing plan is ready
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6838fe1c43/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB']
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6838fe1c43/metadata.json]
> test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6838fe1c43]
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6838fe1c43']
> test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6838fe1c43']
> test-io-repertoires-agg.R: 
> test-io-repertoires-agg.R: -- Summary 
> test-io-repertoires-agg.R: i Time elapsed: 1.65 secs
> test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e68244d3dd2.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683ed56f74/annotations.parquet]
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683ed56f74/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683ed56f74]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683ed56f74']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683ed56f74']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 0.33 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e688d01d35.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 1.43 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/snapshots/baseline/v001']
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")]
> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686b046559/annotations.parquet]
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686b046559/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686b046559]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v002']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686b046559']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686b046559']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/snapshots/baseline/v002']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")]
> test-io-repertoires-counts.R: i Time elapsed: 0.32 secs
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/snapshots/baseline/v001']
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 

> test-io-immundata.R: v All files have the same extension
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6820a71b0f.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 
> test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6829f34479/annotations.parquet]
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 1.45 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001']
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6829f34479/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6829f34479]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6829f34479']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6829f34479']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 1.63 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R:   2.
> test-io-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e684ce9207.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Preprocessing the data 

> test-io-immundata.R:   1. exclude_columns
> test-io-immundata.R:   2. filter_nonproductive
> test-io-immundata.R: v Preprocessing plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e684aac7e38/annotations.parquet]
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e684aac7e38/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e684aac7e38]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e684aac7e38']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e684aac7e38']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 2.09 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e686f447fd6.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Postprocessing the data 

> test-io-immundata.R:   1. prefix_barcodes
> test-io-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-immundata.R: v Postprocessing plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a486c564999/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a486c564999/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a486c564999]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a486c564999']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a486c564999']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 3.1 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68958555d/annotations.parquet]
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68958555d/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68958555d]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68958555d']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68958555d']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 1.93 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 

> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6812732d4e.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 

> test-io-immundata.R: i Time elapsed: 1.4 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB']
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\baseline\v001']
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB']
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB\snapshots\baseline\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectB\snapshots\baseline\v001']
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 

> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681162706/annotations.parquet]
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681162706/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681162706]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681162706']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681162706']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 1.57 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6870cc538d.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685cd22dae/annotations.parquet]
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685cd22dae/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685cd22dae]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685cd22dae']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685cd22dae']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 0.16 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6824c9543b.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 

> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 

> test-io-immundata.R: i Time elapsed: 1.51 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\ops\v001]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\imd_snap_tests\projectA\snapshots\ops\v001']
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 
> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R:   2.
> test-io-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Preprocessing the data 

> test-io-immundata.R:   1. exclude_columns
> test-io-immundata.R:   2. filter_nonproductive
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6828b31dcf/annotations.parquet]
> test-io-immundata.R: v Preprocessing plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 
> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6828b31dcf/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6828b31dcf]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6828b31dcf']
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6828b31dcf']
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 1.54 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Reading repertoire data 
> test-io-repertoires-counts.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6824c9543b.tsv
> test-io-repertoires-counts.R: i Checking if all files are of the same type
> test-io-repertoires-counts.R: v All files have the same extension
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Aggregating the data to receptors 
> test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822a63ecb/annotations.parquet]
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Postprocessing the data 

> test-io-immundata.R:   1. prefix_barcodes
> test-io-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-immundata.R: v Postprocessing plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d2e7555/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d2e7555/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d2e7555]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d2e7555']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a481d2e7555']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 
> test-io-immundata.R: i Time elapsed: 3.11 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-io-immundata.R: 
> test-io-immundata.R: -- Reading repertoire data 

> test-io-immundata.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-immundata.R:   2.
> test-io-immundata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-immundata.R: i Checking if all files are of the same type
> test-io-immundata.R: v All files have the same extension
> test-io-immundata.R: 
> test-io-immundata.R: -- Renaming the columns and schemas 

> test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822a63ecb/metadata.json]
> test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822a63ecb]
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822a63ecb']
> test-io-immundata.R: v Renaming is finished
> test-io-immundata.R: 
> test-io-immundata.R: -- Preprocessing the data 
> test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6822a63ecb']
> test-io-immundata.R:   1. exclude_columns
> test-io-repertoires-counts.R: 
> test-io-repertoires-counts.R: -- Summary 
> test-io-repertoires-counts.R: i Time elapsed: 2.4 secs
> test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")]
> test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors
> test-io-immundata.R:   2. filter_nonproductive
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Reading repertoire data 
> test-io-repertoires-files.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-files.R: i Checking if all files are of the same type
> test-io-repertoires-files.R: v All files have the same extension
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Renaming the columns and schemas 

> test-io-repertoires-files.R: v Renaming is finished
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Aggregating the data to receptors 

> test-io-repertoires-files.R: i No locus information found
> test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-immundata.R: v Preprocessing plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Aggregating the data to receptors 

> test-io-immundata.R: i No locus information found
> test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68f7b3c84/annotations.parquet]
> test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68f7b3c84/metadata.json]
> test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68f7b3c84]
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68f7b3c84']
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68f7b3c84']
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Summary 

> test-io-repertoires-files.R: i Time elapsed: 1.34 secs
> test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Reading repertoire data 
> test-io-repertoires-files.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-files.R:   2.
> test-io-repertoires-files.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-files.R: i Checking if all files are of the same type
> test-io-repertoires-files.R: v All files have the same extension
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Renaming the columns and schemas 

> test-io-repertoires-files.R: v Renaming is finished
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Aggregating the data to receptors 

> test-io-repertoires-files.R: i No locus information found
> test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Postprocessing the data 

> test-io-immundata.R:   1. prefix_barcodes
> test-io-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-immundata.R: v Postprocessing plan is ready
> test-io-immundata.R: 
> test-io-immundata.R: -- Saving the newly created ImmunData to disk 
> test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48375d3869/annotations.parquet]
> test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48375d3869/metadata.json]
> test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48375d3869]
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48375d3869']
> test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a48375d3869']
> test-io-immundata.R: 
> test-io-immundata.R: -- Summary 

> test-io-immundata.R: i Time elapsed: 3.04 secs
> test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Reading repertoire data 

> test-io-repertoires-processing.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-processing.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R: v All files have the same extension
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Renaming the columns and schemas 

> test-io-repertoires-processing.R: v Renaming is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Preprocessing the data 
> test-io-repertoires-processing.R:   1. exclude_columns
> test-io-repertoires-processing.R: v Preprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating the data to receptors 
> test-io-repertoires-processing.R: i No locus information found
> test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e682541106a/annotations.parquet]
> test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e682541106a/metadata.json]
> test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e682541106a]
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e682541106a']
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e682541106a']
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Summary 
> test-io-repertoires-files.R: i Time elapsed: 2.58 secs
> test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Reading repertoire data 
> test-io-repertoires-files.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-files.R:   2.
> test-io-repertoires-files.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-files.R: i Checking if all files are of the same type
> test-io-repertoires-files.R: v All files have the same extension
> test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Postprocessing the data 
> test-io-repertoires-processing.R:   1. prefix_barcodes
> test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-processing.R: v Postprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Renaming the columns and schemas 
> test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude/annotations.parquet]
> test-io-repertoires-files.R: v Renaming is finished
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Aggregating the data to receptors 

> test-io-repertoires-files.R: i No locus information found
> test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude/metadata.json]
> test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude]
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude']
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude']
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Summary 
> test-io-repertoires-processing.R: i Time elapsed: 1.55 secs
> test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Reading repertoire data 
> test-io-repertoires-processing.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-processing.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R: v All files have the same extension
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Renaming the columns and schemas 
> test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene
> test-io-repertoires-processing.R: v Renaming is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Preprocessing the data 
> test-io-repertoires-processing.R:   1. exclude_columns
> test-io-repertoires-processing.R:   2. filter_nonproductive
> test-io-repertoires-processing.R: v Preprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating the data to receptors 
> test-io-repertoires-processing.R: i No locus information found
> test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Postprocessing the data 
> test-io-repertoires-processing.R:   1. prefix_barcodes
> test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-processing.R: v Postprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-rename/annotations.parquet]
> test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68761069ad/annotations.parquet]
> test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-rename/metadata.json]
> test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-rename]
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-rename']
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-rename']
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Summary 

> test-io-repertoires-processing.R: i Time elapsed: 1.82 secs
> test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL]
> test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Reading repertoire data 
> test-io-repertoires-processing.R:   1.
> test-io-repertoires-processing.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-processing.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R: v All files have the same extension
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Renaming the columns and schemas 

> test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene
> test-io-repertoires-processing.R: v Renaming is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Preprocessing the data 
> test-io-repertoires-processing.R:   1. exclude_columns
> test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68761069ad/metadata.json]
> test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68761069ad]
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68761069ad']
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68761069ad']
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Summary 
> test-io-repertoires-files.R: i Time elapsed: 2.48 secs
> test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-processing.R: v Preprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating the data to receptors 
> test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-repertoires-processing.R: i No locus information found
> test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-files.R: Rows: 2 Columns: 4
> test-io-repertoires-files.R: -- Column specification --------------------------------------------------------
> test-io-repertoires-files.R: Delimiter: "\t"
> test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires-files.R: v Metadata parsed successfully
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Reading repertoire data 
> test-io-repertoires-files.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-files.R:   2.
> test-io-repertoires-files.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-files.R: i Checking if all files are of the same type
> test-io-repertoires-files.R: v All files have the same extension
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Renaming the columns and schemas 

> test-io-repertoires-files.R: v Renaming is finished
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Aggregating the data to receptors 

> test-io-repertoires-files.R: i No locus information found
> test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Postprocessing the data 
> test-io-repertoires-processing.R:   1. prefix_barcodes
> test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-processing.R: v Postprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude-rename/annotations.parquet]
> test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude-rename/metadata.json]
> test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude-rename]
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude-rename']
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-exclude-rename']
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Summary 
> test-io-repertoires-processing.R: i Time elapsed: 1.47 secs
> test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL]
> test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Reading repertoire data 
> test-io-repertoires-processing.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-processing.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R: v All files have the same extension
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Renaming the columns and schemas 
> test-io-repertoires-processing.R: v Renaming is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Preprocessing the data 
> test-io-repertoires-processing.R:   1. exclude_columns
> test-io-repertoires-processing.R:   2. filter_nonproductive
> test-io-repertoires-processing.R: v Preprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating the data to receptors 

> test-io-repertoires-processing.R: i No locus information found
> test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Postprocessing the data 

> test-io-repertoires-processing.R:   1. prefix_barcodes
> test-io-repertoires-files.R: v Joining plan is ready
> test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-processing.R: v Postprocessing plan is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686c57177f/annotations.parquet]
> test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet]
> test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json]
> test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k]
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k']
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k']
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Summary 

> test-io-repertoires-processing.R: i Time elapsed: 1.71 secs
> test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors
> test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686c57177f/metadata.json]
> test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686c57177f]
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686c57177f']
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e686c57177f']
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Summary 
> test-io-repertoires-files.R: i Time elapsed: 3.17 secs
> test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-repertoires-files.R: Rows: 2 Columns: 4
> test-io-repertoires-processing.R: Rows: 1000 Columns: 40
> test-io-repertoires-files.R: -- Column specification --------------------------------------------------------
> test-io-repertoires-files.R: Delimiter: "\t"
> test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires-processing.R: -- Column specification --------------------------------------------------------
> test-io-repertoires-processing.R: Delimiter: "\t"
> test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal...
> test-io-repertoires-processing.R: dbl  (5): clone_id, v_score, d_score, j_score, counts
> test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_...
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires-files.R: v Metadata parsed successfully
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Reading repertoire data 
> test-io-repertoires-files.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Reading repertoire data 

> test-io-repertoires-files.R:   2.
> test-io-repertoires-files.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-files.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-files.R: v All files have the same extension
> test-io-repertoires-processing.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R: v All files have the same extension
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Renaming the columns and schemas 
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Renaming the columns and schemas 
> test-io-repertoires-processing.R: v Renaming is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating the data to receptors 
> test-io-repertoires-processing.R: i No locus information found
> test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-files.R: v Renaming is finished
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Aggregating the data to receptors 

> test-io-repertoires-files.R: i No locus information found
> test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Postprocessing the data 
> test-io-repertoires-processing.R:   1. prefix_barcodes
> test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-processing.R: v Postprocessing plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet]
> test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json]
> test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k]
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k']
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k']
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Summary 
> test-io-repertoires-processing.R: i Time elapsed: 1.32 secs
> test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors
> test-io-repertoires-processing.R: Rows: 1000 Columns: 40
> test-io-repertoires-processing.R: -- Column specification --------------------------------------------------------
> test-io-repertoires-processing.R: Delimiter: "\t"
> test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal...
> test-io-repertoires-processing.R: dbl  (5): clone_id, v_score, d_score, j_score, counts
> test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_...
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires-processing.R: Rows: 2 Columns: 4
> test-io-repertoires-processing.R: -- Column specification --------------------------------------------------------
> test-io-repertoires-processing.R: Delimiter: "\t"
> test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires-processing.R: v Metadata parsed successfully
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Reading repertoire data 
> test-io-repertoires-processing.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-processing.R:   2.
> test-io-repertoires-processing.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-processing.R: i Checking if all files are of the same type
> test-io-repertoires-processing.R: v All files have the same extension
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Renaming the columns and schemas 

> test-io-repertoires-processing.R: v Renaming is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating the data to receptors 
> test-io-repertoires-processing.R: i No locus information found
> test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-io-repertoires-files.R: v Joining plan is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681ced6d5d/annotations.parquet]
> test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681ced6d5d/metadata.json]
> test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681ced6d5d]
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681ced6d5d']
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e681ced6d5d']
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Summary 

> test-io-repertoires-files.R: i Time elapsed: 3.14 secs
> test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Reading repertoire data 
> test-io-repertoires-files.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-files.R:   2.
> test-io-repertoires-files.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires-files.R: i Checking if all files are of the same type
> test-io-repertoires-files.R: v All files have the same extension
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Renaming the columns and schemas 

> test-io-repertoires-files.R: v Renaming is finished
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Aggregating the data to receptors 

> test-io-repertoires-files.R: i No locus information found
> test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-io-repertoires-processing.R: v Joining plan is ready
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Aggregating repertoires... 

> test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column 
> test-io-repertoires-files.R: v Joining plan is ready
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864794fc8/annotations.parquet]
> test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864794fc8/metadata.json]
> test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864794fc8]
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864794fc8']
> test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6864794fc8']
> test-io-repertoires-files.R: 
> test-io-repertoires-files.R: -- Summary 

> test-io-repertoires-files.R: i Time elapsed: 3.04 secs
> test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Reading repertoire data 

> test-io-repertoires-schema-paired.R:   1.
> test-io-repertoires-schema-paired.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz
> test-io-repertoires-schema-paired.R: i Checking if all files are of the same type
> test-io-repertoires-schema-paired.R: v All files have the same extension
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors 

> test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-processing.R: v Aggregation is finished
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4815ce23ee/annotations.parquet]
> test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4815ce23ee/metadata.json]
> test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4815ce23ee]
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4815ce23ee']
> test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4815ce23ee']
> test-io-repertoires-processing.R: 
> test-io-repertoires-processing.R: -- Summary 
> test-io-repertoires-processing.R: i Time elapsed: 15.47 secs
> test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy]
> test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Reading repertoire data 
> test-io-repertoires-schema-single.R:   1.
> test-io-repertoires-schema-single.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz
> test-io-repertoires-schema-single.R: i Checking if all files are of the same type
> test-io-repertoires-schema-single.R: v All files have the same extension
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a481c851b42/annotations.parquet]
> test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a481c851b42/metadata.json]
> test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a481c851b42]
> test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a481c851b42']
> test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a481c851b42']
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Summary 
> test-io-repertoires-schema-single.R: i Time elapsed: 3.39 secs
> test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Reading repertoire data 

> test-io-repertoires-schema-single.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4856915730.tsv
> test-io-repertoires-schema-single.R: i Checking if all files are of the same type
> test-io-repertoires-schema-single.R: v All files have the same extension
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a48218159e7/annotations.parquet]
> test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a48218159e7/metadata.json]
> test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a48218159e7]
> test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a48218159e7']
> test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a48218159e7']
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Summary 
> test-io-repertoires-schema-single.R: i Time elapsed: 0.36 secs
> test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Reading repertoire data 
> test-io-repertoires-schema-single.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\file6a4852ef460e.tsv
> test-io-repertoires-schema-single.R: i Checking if all files are of the same type
> test-io-repertoires-schema-single.R: v All files have the same extension
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
> test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4820d757ac/annotations.parquet]
> test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4820d757ac/metadata.json]
> test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4820d757ac]
> test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4820d757ac']
> test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test_immundata_6a4820d757ac']
> test-io-repertoires-schema-single.R: 
> test-io-repertoires-schema-single.R: -- Summary 
> test-io-repertoires-schema-single.R: i Time elapsed: 0.34 secs
> test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
> test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Reading repertoire data 

> test-io-repertoires-schema-table.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema-table.R: i Checking if all files are of the same type
> test-io-repertoires-schema-table.R: v All files have the same extension
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Renaming the columns and schemas 

> test-io-repertoires-schema-table.R: v Renaming is finished
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Preprocessing the data 

> test-io-repertoires-schema-table.R:   1. exclude_columns
> test-io-repertoires-schema-table.R:   2. filter_nonproductive
> test-io-repertoires-schema-table.R: v Preprocessing plan is ready
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Aggregating the data to receptors 

> test-io-repertoires-schema-table.R: i No locus information found
> test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Postprocessing the data 
> test-io-repertoires-schema-table.R:   1. prefix_barcodes
> test-io-repertoires-schema-table.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires-schema-table.R: v Postprocessing plan is ready
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-no-barcodes/annotations.parquet]
> test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-no-barcodes/metadata.json]
> test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683b605798/annotations.parquet]
> test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-no-barcodes]
> test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-no-barcodes']
> test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpc9cxJu\test-no-barcodes']
> test-io-repertoires-schema-table.R: 
> test-io-repertoires-schema-table.R: -- Summary 
> test-io-repertoires-schema-table.R: i Time elapsed: 1.73 secs
> test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
> test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 
> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 
> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 
> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 

> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 
> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 
> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 

> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 
> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 

> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 
> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 

> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 

> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 
> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 

> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 
> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 
> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 
> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 

> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 
> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 

> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 

> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 
> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 

> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 

> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683b605798/metadata.json]
> test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683b605798]
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683b605798']
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e683b605798']
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Summary 

> test-io-repertoires-schema-paired.R: i Time elapsed: 21.4 secs
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")]
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Reading repertoire data 
> test-io-repertoires-schema-paired.R:   1.
> test-io-repertoires-schema-paired.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz
> test-io-repertoires-schema-paired.R: i Checking if all files are of the same type
> test-io-repertoires-schema-paired.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 
> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 
> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 

> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 

> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Reading repertoire data 

> test-io-repertoires-schema.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires-schema.R: i Checking if all files are of the same type
> test-io-repertoires-schema.R: v All files have the same extension
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Renaming the columns and schemas 

> test-io-repertoires-schema.R: v Renaming is finished
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Preprocessing the data 

> test-io-repertoires-schema.R:   1. exclude_columns
> test-io-repertoires-schema.R:   2. filter_nonproductive
> test-io-repertoires-schema.R: v Preprocessing plan is ready
> test-io-repertoires-schema.R: 
> test-io-repertoires-schema.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68429e1286/annotations.parquet]
> test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68429e1286/metadata.json]
> test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68429e1286]
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68429e1286']
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e68429e1286']
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Summary 
> test-io-repertoires-schema-paired.R: i Time elapsed: 19.59 secs
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")]
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Reading repertoire data 

> test-io-repertoires-schema-paired.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e686808c83.tsv
> test-io-repertoires-schema-paired.R: i Checking if all files are of the same type
> test-io-repertoires-schema-paired.R: v All files have the same extension
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk 

> test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6849255e9d/annotations.parquet]
> test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6849255e9d/metadata.json]
> test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6849255e9d]
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6849255e9d']
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e6849255e9d']
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Summary 
> test-io-repertoires-schema-paired.R: i Time elapsed: 1.41 secs
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Reading repertoire data 
> test-io-repertoires-schema-paired.R:   1. D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\file8e6864c377c1.tsv
> test-io-repertoires-schema-paired.R: i Checking if all files are of the same type
> test-io-repertoires-schema-paired.R: v All files have the same extension
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors 
> test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
> test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
> test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk 
> test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685d4e2b20/annotations.parquet]
> test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685d4e2b20/metadata.json]
> test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685d4e2b20]
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685d4e2b20']
> test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_16_11_15_17_8460\Rtmpyu6Shs\test_immundata_8e685d4e2b20']
> test-io-repertoires-schema-paired.R: 
> test-io-repertoires-schema-paired.R: -- Summary 

> test-io-repertoires-schema-paired.R: i Time elapsed: 1.87 secs
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
> test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 351 ]
> 
> proc.time()
   user  system elapsed 
   4.51    0.45  158.25