* using log directory 'd:/RCompile/CRANincoming/R-devel/immundata.Rcheck'
* using R Under development (unstable) (2026-03-14 r89623 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-03-15 20:45:28 UTC
* checking for file 'immundata/DESCRIPTION' ... OK
* this is package 'immundata' version '0.0.6'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... OK
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'immundata' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [178s] ERROR
  Running 'testthat.R' [178s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > 
  > library(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: 4.
  → 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-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: 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-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-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-annotate-barcodes.R:   2. filter_nonproductive
  > 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: 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 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 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc29f212f4/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-barcodes.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc29f212f4/metadata.json]
  > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc29f212f4]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc29f212f4']
  > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc29f212f4']
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Summary 
  > test-annotate-barcodes.R: i Time elapsed: 2.81 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: 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_15_21_45_17_13593\Rtmp6NsfJN\file729c524f4ddd/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c524f4ddd/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c524f4ddd]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c524f4ddd']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c524f4ddd']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.39 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: 
  > 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-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:   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 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_15_21_45_17_13593\Rtmp6NsfJN\file729c211927a2/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c211927a2/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c211927a2]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c211927a2']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c211927a2']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.29 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc3f496bb4/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3f496bb4/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3f496bb4]
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3f496bb4']
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3f496bb4']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.12 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_15_21_45_17_13593\Rtmp6NsfJN\file729c370f655a/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c370f655a/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c370f655a]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c370f655a']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c370f655a']
  > 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-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_15_21_45_17_13593\RtmpKmMb7A\file6ccc150951ef/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc150951ef/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc150951ef]
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc150951ef']
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc150951ef']
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.99 secs
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > 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-annotate-external.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-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: 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: 
  > test-annotate-external.R: -- Renaming the columns and schemas 
  > test-agg-strata.R:   2. filter_nonproductive
  > 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 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 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-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_15_21_45_17_13593\RtmpKmMb7A\file6ccc1a132417/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc1a132417/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc1a132417]
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc1a132417']
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc1a132417']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.04 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 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-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 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_15_21_45_17_13593\Rtmp6NsfJN\file729c2ba379dc/annotations.parquet]
  > 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_15_21_45_17_13593\Rtmp6NsfJN\file729c2ba379dc/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2ba379dc]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2ba379dc']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2ba379dc']
  > 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-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_15_21_45_17_13593\RtmpKmMb7A\file6cccdd4df8/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6cccdd4df8/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6cccdd4df8]
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6cccdd4df8']
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6cccdd4df8']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.01 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-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: 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 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_15_21_45_17_13593\Rtmp6NsfJN\file729ce6095d/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ce6095d/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ce6095d]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ce6095d']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ce6095d']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.83 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc77bf397a/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_15_21_45_17_13593\RtmpKmMb7A\file6ccc77bf397a/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc77bf397a]
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc77bf397a']
  > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc77bf397a']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.98 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-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 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_15_21_45_17_13593\Rtmp6NsfJN\file729c4bc21c32/annotations.parquet]
  > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c4bc21c32/metadata.json]
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Postprocessing the data 
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c4bc21c32]
  > 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-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c4bc21c32']
  > 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc38d43c4c/annotations.parquet]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c4bc21c32']
  > 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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc38d43c4c/metadata.json]
  > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc38d43c4c]
  > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc38d43c4c']
  > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc38d43c4c']
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Summary 
  > test-annotate-receptors.R: i Time elapsed: 2.97 secs
  > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-receptors.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_15_21_45_17_13593\RtmpKmMb7A\file6ccc67f64929/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc67f64929/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc67f64929]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc67f64929']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc67f64929']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 3.85 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-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: 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 Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > 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 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_15_21_45_17_13593\Rtmp6NsfJN\file729c783e350e/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c783e350e/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c783e350e]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c783e350e']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c783e350e']
  > 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-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_15_21_45_17_13593\RtmpKmMb7A\file6ccc8255b28/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc8255b28/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc8255b28]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc8255b28']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc8255b28']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 3.88 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-agg-strata.R: Rows: 2 Columns: 4
  > 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: -- 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-compute-collect-immundata.R:   2. filter_nonproductive
  > 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 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 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-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 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc3359e0/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_15_21_45_17_13593\Rtmp6NsfJN\file729c620a42a2/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3359e0/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3359e0]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3359e0']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3359e0']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 3.8 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-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c620a42a2/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c620a42a2]
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c620a42a2']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c620a42a2']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.8 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: 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: 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-compute-collect-immundata.R: v Preprocessing plan is ready
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: i No locus information found
  > test-agg-strata.R: v All files have the same extension
  > test-compute-collect-immundata.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-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-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 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc4b9029fc/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc4b9029fc/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc4b9029fc]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc4b9029fc']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc4b9029fc']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 3.81 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-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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc73885e35.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is 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_15_21_45_17_13593\Rtmp6NsfJN\file729ceb924da/annotations.parquet]
  > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc40b4528/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc40b4528/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc40b4528]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc40b4528']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc40b4528']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.33 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-downsample.R: v Loaded ImmunData with [8] chains and [8] receptors
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ceb924da/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ceb924da]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ceb924da']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729ceb924da']
  > 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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc13cf6d54.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i No locus information found
  > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with 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-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc635167c/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc635167c/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc635167c]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc635167c']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc635167c']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.15 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL]
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors
  > 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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc10bf1080.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
  > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is 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-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1e3b5842/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-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1e3b5842/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1e3b5842]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1e3b5842']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1e3b5842']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 2.33 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-downsample.R: v Loaded ImmunData with [12] chains and [6] receptors
  > 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_15_21_45_17_13593\Rtmp6NsfJN\file729c500c326e/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c500c326e/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c500c326e]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c500c326e']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c500c326e']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.9 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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1.
  > test-downsample.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to 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-downsample.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only
  > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is 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-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_15_21_45_17_13593\Rtmp6NsfJN\file729c72a51857/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c72a51857/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c72a51857]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c72a51857']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c72a51857']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.8 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-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_15_21_45_17_13593\Rtmp6NsfJN\file729c78bb220d/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c78bb220d/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c78bb220d]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c78bb220d']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c78bb220d']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.77 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-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_15_21_45_17_13593\Rtmp6NsfJN\file729c98730d2/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c98730d2/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c98730d2]
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c98730d2']
  > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c98730d2']
  > 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-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-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_15_21_45_17_13593\Rtmp6NsfJN\file729c6f41360/annotations.parquet]
  > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c6f41360/metadata.json]
  > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c6f41360]
  > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c6f41360']
  > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c6f41360']
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Summary 
  > test-filter-barcodes.R: i Time elapsed: 2.95 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-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-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-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6cccba96a62/annotations.parquet]
  > 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_15_21_45_17_13593\Rtmp6NsfJN\file729c377258b7/annotations.parquet]
  > test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c377258b7/metadata.json]
  > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c377258b7]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c377258b7']
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c377258b7']
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Summary 
  > test-filter-immundata-exact.R: i Time elapsed: 2.94 secs
  > 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-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Reading repertoire data 
  > 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-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-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-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-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6cccba96a62/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6cccba96a62]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6cccba96a62']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6cccba96a62']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 20.97 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")]
  > test-downsample.R: v Loaded ImmunData with [1814] chains and [901] receptors
  > 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_15_21_45_17_13593\Rtmp6NsfJN\file729c807367/annotations.parquet]
  > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c807367/metadata.json]
  > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c807367]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c807367']
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c807367']
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Summary 
  > test-filter-immundata-hamm.R: i Time elapsed: 3.1 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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc6eb75fd9.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc73b648cf/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc73b648cf/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc73b648cf]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc73b648cf']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc73b648cf']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.33 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-downsample.R: v Loaded ImmunData with [8] chains and [6] 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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
  > test-downsample.R:   2.
  > test-downsample.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Renaming the columns and schemas 
  > test-downsample.R: v Renaming is finished
  > test-downsample.R: 
  > test-downsample.R: -- Preprocessing the data 
  > test-downsample.R:   1. exclude_columns
  > test-downsample.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-downsample.R: v Preprocessing plan is ready
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i No locus information found
  > test-downsample.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_15_21_45_17_13593\Rtmp6NsfJN\file729c2aca4c12/annotations.parquet]
  > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Postprocessing the data 
  > test-downsample.R:   1. prefix_barcodes
  > test-downsample.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-downsample.R: v Postprocessing plan is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc26542a99/annotations.parquet]
  > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2aca4c12/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2aca4c12]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2aca4c12']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2aca4c12']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 2.99 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-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc26542a99/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc26542a99]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc26542a99']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc26542a99']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 2.99 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-downsample.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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc4f6974b7.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > 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-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc592e6843/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc592e6843/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc592e6843]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc592e6843']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc592e6843']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.33 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-downsample.R: v Loaded ImmunData with [6] chains and [6] receptors
  > 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-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc1c4d5fe2.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i No locus information found
  > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible
  > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7da11cbb/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7da11cbb/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7da11cbb]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7da11cbb']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7da11cbb']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.15 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL]
  > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors
  > test-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc18649c9.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i No locus information found
  > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible
  > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc26af3191/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc26af3191/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc26af3191]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc26af3191']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc26af3191']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.15 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL]
  > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors
  > test-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv
  > test-downsample.R:   2.
  > test-downsample.R:   D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Renaming the columns and schemas 
  > test-downsample.R: v Renaming is finished
  > test-downsample.R: 
  > test-downsample.R: -- Preprocessing the data 
  > test-downsample.R:   1. exclude_columns
  > test-downsample.R:   2. filter_nonproductive
  > 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_15_21_45_17_13593\Rtmp6NsfJN\file729c24583f5c/annotations.parquet]
  > test-downsample.R: v Preprocessing plan is ready
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i No locus information found
  > test-downsample.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c24583f5c/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c24583f5c]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c24583f5c']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c24583f5c']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 3.03 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: 
  > 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-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-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-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Postprocessing the data 
  > test-downsample.R:   1. prefix_barcodes
  > test-downsample.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-downsample.R: v Postprocessing plan is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3c0184/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3c0184/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3c0184]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3c0184']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc3c0184']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 2.95 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-downsample.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-downsample.R: 
  > test-downsample.R: -- Reading repertoire data 
  > test-downsample.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc5faf45ea.tsv
  > test-downsample.R: i Checking if all files are of the same type
  > test-downsample.R: v All files have the same extension
  > test-downsample.R: 
  > test-downsample.R: -- Aggregating the data to receptors 
  > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-downsample.R: 
  > test-downsample.R: -- Saving the newly created ImmunData to disk 
  > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc299d6e36/annotations.parquet]
  > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc299d6e36/metadata.json]
  > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc299d6e36]
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc299d6e36']
  > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc299d6e36']
  > test-downsample.R: 
  > test-downsample.R: -- Summary 
  > test-downsample.R: i Time elapsed: 0.32 secs
  > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-downsample.R: v Loaded ImmunData with [6] chains and [4] receptors
  > 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 
  Saving _problems/test-downsample-35.R
  Saving _problems/test-downsample-83.R
  Saving _problems/test-downsample-216.R
  Saving _problems/test-downsample-312.R
  Saving _problems/test-downsample-348.R
  Saving _problems/test-downsample-381.R
  Saving _problems/test-downsample-436.R
  > test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c458f36e/annotations.parquet]
  > 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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c458f36e/metadata.json]
  > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c458f36e]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c458f36e']
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c458f36e']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Summary 
  > test-filter-immundata-regex.R: i Time elapsed: 2.98 secs
  > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata.R:   2. filter_nonproductive
  > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > 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-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 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-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: 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: 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_15_21_45_17_13593\Rtmp6NsfJN\file729c3ac4626d/annotations.parquet]
  > 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc121947b/annotations.parquet]
  > test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c3ac4626d/metadata.json]
  > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c3ac4626d]
  > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c3ac4626d']
  > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c3ac4626d']
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Summary 
  > test-filter-receptors.R: i Time elapsed: 2.98 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-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc121947b/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc121947b]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc121947b']
  > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc121947b']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 3.83 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-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: 
  > 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-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_15_21_45_17_13593\Rtmp6NsfJN\legacy_v1_729c72677895/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\legacy_v1_729c72677895/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\legacy_v1_729c72677895]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\legacy_v1_729c72677895']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\legacy_v1_729c72677895']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.34 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 Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\legacy_v1_729c72677895']
  > 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-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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > 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-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-filter-immundata.R:   1. prefix_barcodes
  > test-io-immundata.R: i Time elapsed: 1.31 secs
  > 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-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc391a7c2e/annotations.parquet]
  > 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-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc391a7c2e/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc391a7c2e]
  > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc391a7c2e']
  > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc391a7c2e']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 2.97 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.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc29056f21.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5dab2e68/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5dab2e68/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5dab2e68]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5dab2e68']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5dab2e68']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.33 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.35 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-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc324c6a19.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: 
  > 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-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: 
  > 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: 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc57ea785d/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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.36 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc57ea785d/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc57ea785d]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc57ea785d']
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc57ea785d']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.47 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-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-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_15_21_45_17_13593\RtmpKmMb7A\file6ccc6b8b1dbd.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc68a1b8c/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc68a1b8c/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc68a1b8c]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc68a1b8c']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc68a1b8c']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.46 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc3c35414.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: -- 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_15_21_45_17_13593\Rtmp6NsfJN\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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc118d4d6d/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 3.25 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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc118d4d6d/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc118d4d6d]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc118d4d6d']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc118d4d6d']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.49 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-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc2b29583f.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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.34 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001']
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc432d6a9/annotations.parquet]
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc432d6a9/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc432d6a9]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc432d6a9']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc432d6a9']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.42 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc365e3dac.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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002/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-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]
  > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5a5c420f/annotations.parquet]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002']
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\treated\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\treated\v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB/metadata.json]
  > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5a5c420f/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB]
  > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5a5c420f]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5a5c420f']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc5a5c420f']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.39 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-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
  Saving _problems/test-io-repertoires-agg-60.R
  Saving _problems/test-io-repertoires-agg-66.R
  Saving _problems/test-io-repertoires-agg-84.R
  Saving _problems/test-io-repertoires-agg-92.R
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-repertoires-counts.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc26645953.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccce3733b1/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccce3733b1/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccce3733b1]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccce3733b1']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccce3733b1']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.34 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc7ee77f1d.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc6d767ca7/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc6d767ca7/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc6d767ca7]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc6d767ca7']
  > 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-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc6d767ca7']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-repertoires-counts.R: i Time elapsed: 0.35 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 [3] 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc1c90ace.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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.35 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v002']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/snapshots/baseline/v002']
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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: 
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc67834423/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc67834423/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc67834423]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc67834423']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc67834423']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.48 secs
  > 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-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-repertoires-counts.R: v Loaded ImmunData with [6] 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc6742bd8.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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.33 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\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:   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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7a3339b2/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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7a3339b2/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7a3339b2]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7a3339b2']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc7a3339b2']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 2.17 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_15_21_45_17_13593\RtmpKmMb7A\file6ccca91258d.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_15_21_45_17_13593\Rtmp6NsfJN\file729c2d10549a/annotations.parquet]
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4b3748ff/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2d10549a/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2d10549a]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2d10549a']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c2d10549a']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.96 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: 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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4b3748ff/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4b3748ff]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4b3748ff']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4b3748ff']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.38 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-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: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-repertoires-counts.R:   1. D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\file6ccc1ce26c25.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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4d336438/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.5 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB']
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\baseline\v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB']
  > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectB\snapshots\baseline\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4d336438/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4d336438]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4d336438']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc4d336438']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.71 secs
  > 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 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc505f6d20.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13681b09/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13681b09/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13681b09]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13681b09']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13681b09']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.17 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc6a9a2004.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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.32 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_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet]
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc49021a57/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\imd_snap_tests\projectA\snapshots\ops\v001]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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-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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc49021a57/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc49021a57]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc49021a57']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc49021a57']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 2.5 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc6a9a2004.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: -- 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_15_21_45_17_13593\Rtmp6NsfJN\file729c137450b/annotations.parquet]
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc19c1d76/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c137450b/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c137450b]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c137450b']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c137450b']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.99 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-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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc19c1d76/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc19c1d76]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc19c1d76']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc19c1d76']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.98 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-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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc53ab31d4/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc53ab31d4/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc53ab31d4]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc53ab31d4']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc53ab31d4']
  > 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_15_21_45_17_13593\Rtmp6NsfJN\file729c16cf136d/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c16cf136d/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c16cf136d]
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c16cf136d']
  > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\file729c16cf136d']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.99 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
  Saving _problems/test-io-immundata-99.R
  > 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13254d4a/annotations.parquet]
  > 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_15_21_45_17_13593\Rtmp6NsfJN\test-exclude/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13254d4a/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13254d4a]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13254d4a']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc13254d4a']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 2.45 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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.41 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-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: 
  > 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_15_21_45_17_13593\Rtmp6NsfJN\test-rename/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-rename/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-rename]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-rename']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-rename']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.67 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-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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3a91568c/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3a91568c/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3a91568c]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3a91568c']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3a91568c']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 2.46 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-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_15_21_45_17_13593\Rtmp6NsfJN\test-exclude-rename/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude-rename/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude-rename]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude-rename']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-exclude-rename']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.4 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-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: 1.67 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-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: 
  > 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-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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc55cf29e8/annotations.parquet]
  > 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: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc55cf29e8/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc55cf29e8]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc55cf29e8']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc55cf29e8']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.18 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-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:\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: 1.33 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3650797b/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3650797b/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3650797b]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3650797b']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc3650797b']
  > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column 
  > 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: 
  > 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 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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc25e928ca/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc25e928ca/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc25e928ca]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc25e928ca']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc25e928ca']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.13 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_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2b954fcc/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2b954fcc/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2b954fcc]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2b954fcc']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2b954fcc']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 19.79 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-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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1a9f1b0f/annotations.parquet]
  > 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_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c6ea254ba/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c6ea254ba/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c6ea254ba]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c6ea254ba']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c6ea254ba']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 3.5 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_15_21_45_17_13593\Rtmp6NsfJN\file729c22cf58ef.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_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c1d5446f9/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c1d5446f9/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c1d5446f9]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c1d5446f9']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c1d5446f9']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 0.31 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_15_21_45_17_13593\Rtmp6NsfJN\file729c3f492740.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_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2cce52d/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2cce52d/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2cce52d]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2cce52d']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test_immundata_729c2cce52d']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 0.31 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_15_21_45_17_13593\Rtmp6NsfJN\test-no-barcodes/annotations.parquet]
  > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-no-barcodes/metadata.json]
  > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-no-barcodes]
  > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\test-no-barcodes']
  > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\Rtmp6NsfJN\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: 1.7 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-paired.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1a9f1b0f/metadata.json]
  > test-io-repertoires-schema.R:   1. exclude_columns
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1a9f1b0f]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1a9f1b0f']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc1a9f1b0f']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 22.04 secs
  > test-io-repertoires-schema.R:   2. filter_nonproductive
  > 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-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: 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: -- 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-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: 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.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc746a2a43/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc746a2a43/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc746a2a43]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc746a2a43']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc746a2a43']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 21.24 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc798542eb.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc37ba3b27/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc37ba3b27/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc37ba3b27]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc37ba3b27']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccc37ba3b27']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 1.44 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_15_21_45_17_13593\RtmpKmMb7A\file6ccc7626719.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_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccceab6c79/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccceab6c79/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccceab6c79]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccceab6c79']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_21_45_17_13593\RtmpKmMb7A\test_immundata_6ccceab6c79']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 1.38 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 12 | WARN 0 | SKIP 0 | PASS 291 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-downsample.R:35:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ──
  Error in `downsample_immundata(idata, n = 2, seed = 100)`: No barcode units were selected. Increase `n`.
  Backtrace:
      ▆
   1. └─immundata::downsample_immundata(idata, n = 2, seed = 100) at test-downsample.R:35:3
   2.   └─cli::cli_abort("No barcode units were selected. Increase `n`.")
   3.     └─rlang::abort(...)
  ── Error ('test-downsample.R:83:3'): downsample_immundata downsampled bulk repertoires by count ──
  Error in `downsample_immundata(idata, n = 5, seed = 42)`: No barcode units were selected. Increase `n`.
  Backtrace:
      ▆
   1. └─immundata::downsample_immundata(idata, n = 5, seed = 42) at test-downsample.R:83:3
   2.   └─cli::cli_abort("No barcode units were selected. Increase `n`.")
   3.     └─rlang::abort(...)
  ── Error ('test-downsample.R:216:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ──
  Error in `select(sampled_receptors, all_of(receptor_join_cols))`: i In argument: `all_of(receptor_join_cols)`.
  Caused by error in `all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `imd_repertoire_id` and `imd_receptor_id` don't exist.
  ── Error ('test-downsample.R:309:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ──
  Error in `downsample_immundata(idata, n = 10, seed = 42)`: No barcode units were selected. Increase `n`.
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(...) at test-downsample.R:309:3
   2. │ └─testthat:::expect_condition_matching_(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─immundata::downsample_immundata(idata, n = 10, seed = 42)
   8.   └─cli::cli_abort("No barcode units were selected. Increase `n`.")
   9.     └─rlang::abort(...)
  ── Error ('test-downsample.R:348:3'): downsample_immundata supports count-mode proportion downsampling ──
  Error in `downsample_immundata(idata, n = 0.5, seed = 101)`: No barcode units were selected. Increase `n`.
  Backtrace:
      ▆
   1. └─immundata::downsample_immundata(idata, n = 0.5, seed = 101) at test-downsample.R:348:3
   2.   └─cli::cli_abort("No barcode units were selected. Increase `n`.")
   3.     └─rlang::abort(...)
  ── Error ('test-downsample.R:381:3'): downsample_immundata is deterministic in count mode with seed ──
  Error in `downsample_immundata(idata, n = 5, seed = 222)`: No barcode units were selected. Increase `n`.
  Backtrace:
      ▆
   1. └─immundata::downsample_immundata(idata, n = 5, seed = 222) at test-downsample.R:381:3
   2.   └─cli::cli_abort("No barcode units were selected. Increase `n`.")
   3.     └─rlang::abort(...)
  ── Error ('test-downsample.R:436:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ──
  Error in `downsample_immundata(idata, n = 2, seed = 33)`: No barcode units were selected. Increase `n`.
  Backtrace:
      ▆
   1. └─immundata::downsample_immundata(idata, n = 2, seed = 33) at test-downsample.R:436:3
   2.   └─cli::cli_abort("No barcode units were selected. Increase `n`.")
   3.     └─rlang::abort(...)
  ── Failure ('test-io-repertoires-agg.R:58:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample1_stats$n_receptors` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Sample1 should have 2 unique receptors
  ── Failure ('test-io-repertoires-agg.R:64:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample2_stats$n_receptors` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Sample2 should have 2 unique receptors
  ── Failure ('test-io-repertoires-agg.R:82:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample1_counts$total_count1[1]` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Shared receptor should have count of 2
  ── Failure ('test-io-repertoires-agg.R:90:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample1_counts$total_count2[1]` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Shared receptor should have count of 2
  ── Failure ('test-io-immundata.R:99:3'): read_repertoires() writes metadata with lineage array and provenance ──
  Expected `metadata_json$provenance$snapshot_root` to equal `file.path(normalized_out, "snapshots")`.
  Differences:
  actual vs expected
  - "D:\\temp\\2026_03_15_21_45_17_13593\\Rtmp6NsfJN\\imd_snap_tests\\projectA\\snapshots"
  + "D:\\temp\\2026_03_15_21_45_17_13593\\Rtmp6NsfJN\\imd_snap_tests\\projectA/snapshots"
  
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 291 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR