• using R version 4.5.3 (2026-03-11 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
• checking for file 'immundata/DESCRIPTION' ... OK
• this is package 'immundata' version '0.0.6'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'immundata' can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s] OK
• checking whether the package can be unloaded cleanly ... [2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s] OK
• checking whether the namespace can be unloaded cleanly ... [3s] OK
• checking loading without being on the library search path ... [3s] OK
• checking whether startup messages can be suppressed ... [3s] 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 ... [9s] OK
• checking Rd files ... [1s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... [4s] OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [257s] ERROR   Running 'testthat.R' [256s] 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: 1.   → 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225/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_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225/metadata.json]   > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225]   > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225']   > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c8ab6225']   > test-annotate-barcodes.R:   > test-annotate-barcodes.R: -- Summary   > test-annotate-barcodes.R: i Time elapsed: 5.44 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_28_18_56_34_11186\RtmpYL630M\file8998462719b1/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998462719b1']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.62 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpYL630M\file899845f14036/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899845f14036']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.56 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b/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_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b/metadata.json]   > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b]   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b']   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c84a1f3b']   > test-annotate-external.R:   > test-annotate-external.R: -- Summary   > test-annotate-external.R: i Time elapsed: 5.48 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpYL630M\file8998329d1e6/annotations.parquet]   > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready   > test-annotate-external.R:   > test-annotate-external.R: -- Postprocessing the data   > test-annotate-external.R: 1. prefix_barcodes   > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-annotate-external.R: v Postprocessing plan is ready   > test-annotate-external.R:   > test-annotate-external.R: -- Saving the newly created ImmunData to disk   > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998329d1e6']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.5 secs   > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c/metadata.json]   > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c]   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c']   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c480e4a8c']   > test-annotate-external.R:   > test-annotate-external.R: -- Summary   > test-annotate-external.R: i Time elapsed: 5.2 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\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: 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-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:   > 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-agg-strata.R: i Checking if all files are of the same type   > test-agg-strata.R: v All files have the same extension   > test-annotate-external.R: 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-annotate-external.R: v Preprocessing plan is ready   > test-annotate-external.R:   > test-annotate-external.R: -- Aggregating the data to receptors   > test-annotate-external.R: i No locus information found   > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R: v Preprocessing plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Aggregating the data to receptors   > test-agg-strata.R: i No locus information found   > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready   > test-annotate-external.R:   > test-annotate-external.R: -- Postprocessing the data   > test-annotate-external.R: 1. prefix_barcodes   > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-annotate-external.R: v Postprocessing plan is ready   > test-annotate-external.R:   > test-annotate-external.R: -- Saving the newly created ImmunData to disk   > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca/annotations.parquet]   > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column   > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca/metadata.json]   > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca]   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca']   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c254b23ca']   > test-annotate-external.R:   > test-annotate-external.R: -- Summary   > test-annotate-external.R: i Time elapsed: 5.08 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-annotate-external.R: i Checking if all files are of the same type   > test-annotate-external.R: v All files have the same extension   > test-annotate-external.R:   > test-annotate-external.R: -- Renaming the columns and schemas   > test-annotate-external.R: v Renaming is finished   > test-annotate-external.R:   > test-annotate-external.R: -- Preprocessing the data   > test-annotate-external.R: 1. exclude_columns   > test-annotate-external.R: 2. filter_nonproductive   > test-agg-strata.R: v Joining plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Postprocessing the data   > test-agg-strata.R: 1. prefix_barcodes   > test-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_28_18_56_34_11186\RtmpYL630M\file8998d360be/annotations.parquet]   > test-annotate-external.R: v Preprocessing plan is ready   > test-annotate-external.R:   > test-annotate-external.R: -- Aggregating the data to receptors   > test-annotate-external.R: i No locus information found   > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998d360be']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.73 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f/annotations.parquet]   > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f/metadata.json]   > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f]   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f']   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2edd5b6f']   > test-annotate-external.R:   > test-annotate-external.R: -- Summary   > test-annotate-external.R: i Time elapsed: 5.12 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-external.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpYL630M\file89987afb7088/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89987afb7088']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.67 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-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready   > 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:   > test-annotate-external.R: -- Postprocessing the data   > test-annotate-external.R: 1. prefix_barcodes   > test-agg-strata.R:   > test-agg-strata.R: -- Reading repertoire data   > 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-agg-strata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-external.R:   > test-annotate-external.R: -- Saving the newly created ImmunData to disk   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-agg-strata.R: i Checking if all files are of the same type   > test-agg-strata.R: v All files have the same extension   > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62/annotations.parquet]   > 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: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62/metadata.json]   > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62]   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62']   > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c46a17b62']   > test-annotate-external.R:   > test-annotate-external.R: -- Summary   > test-annotate-external.R: i Time elapsed: 4.96 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-annotate-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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-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-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready   > test-annotate-receptors.R:   > test-annotate-receptors.R: -- Postprocessing the data   > test-annotate-receptors.R: 1. prefix_barcodes   > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-annotate-receptors.R: v Postprocessing plan is ready   > test-annotate-receptors.R:   > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk   > test-annotate-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf/annotations.parquet]   > 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_28_18_56_34_11186\RtmpYL630M\file899821a65b70/annotations.parquet]   > test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf/metadata.json]   > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf]   > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf']   > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5ee946cf']   > test-annotate-receptors.R:   > test-annotate-receptors.R: -- Summary   > test-annotate-receptors.R: i Time elapsed: 4.92 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-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899821a65b70']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.3 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: 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6/annotations.parquet]   > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6/metadata.json]   > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6]   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6']   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c20fa64b6']   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Summary   > test-compute-collect-immundata.R: i Time elapsed: 6.51 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-compute-collect-immundata.R: i Checking if all files are of the same type   > test-compute-collect-immundata.R: v All files have the same extension   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Renaming the columns and schemas   > test-compute-collect-immundata.R: v Renaming is finished   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Preprocessing the data   > test-compute-collect-immundata.R: 1. exclude_columns   > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column   > test-compute-collect-immundata.R: 2. filter_nonproductive   > test-compute-collect-immundata.R: v Preprocessing plan is ready   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Aggregating the data to receptors   > test-compute-collect-immundata.R: i No locus information found   > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R: v Joining plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Postprocessing the data   > test-agg-strata.R: 1. prefix_barcodes   > test-agg-strata.R: v Postprocessing plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Saving the newly created ImmunData to disk   > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89982c83782c']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.34 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_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13/annotations.parquet]   > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13/metadata.json]   > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13]   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13']   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c21d01e13']   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Summary   > test-compute-collect-immundata.R: i Time elapsed: 6.22 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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: Rows: 2 Columns: 4   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Renaming the columns and schemas   > 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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: 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:   > 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-compute-collect-immundata.R: 2. filter_nonproductive   > 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_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81/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_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b/annotations.parquet]   > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81/metadata.json]   > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81]   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81']   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c72635e81']   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Summary   > test-compute-collect-immundata.R: i Time elapsed: 6.15 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-compute-collect-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984ca3e3b']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.27 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-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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6/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-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6/metadata.json]   > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6]   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6']   > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2791fd6']   > test-compute-collect-immundata.R:   > test-compute-collect-immundata.R: -- Summary   > test-compute-collect-immundata.R: i Time elapsed: 6.32 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-filter-barcodes.R:   > test-filter-barcodes.R: -- Reading repertoire data   > test-agg-strata.R: 1. prefix_barcodes   > test-filter-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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_28_18_56_34_11186\RtmpYL630M\file89984b06b9d/annotations.parquet]   > test-filter-barcodes.R: 2. filter_nonproductive   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984b06b9d']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.42 secs   > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-filter-barcodes.R: v Preprocessing plan is ready   > test-filter-barcodes.R:   > test-filter-barcodes.R: -- Aggregating the data to receptors   > test-filter-barcodes.R: i No locus information found   > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R: 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-agg-strata.R: i Checking if all files are of the same type   > test-agg-strata.R: v All files have the same extension   > test-agg-strata.R:   > test-agg-strata.R: -- Renaming the columns and schemas   > test-agg-strata.R: v Renaming is finished   > test-agg-strata.R:   > test-agg-strata.R: -- Preprocessing the data   > test-agg-strata.R: 1. exclude_columns   > test-agg-strata.R: 2. filter_nonproductive   > test-agg-strata.R: v Preprocessing plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Aggregating the data to receptors   > test-agg-strata.R: i No locus information found   > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-filter-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_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09/annotations.parquet]   > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09/metadata.json]   > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09]   > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09']   > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c36d94b09']   > test-filter-barcodes.R:   > test-filter-barcodes.R: -- Summary   > test-filter-barcodes.R: i Time elapsed: 5.12 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-immundata-exact.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-filter-immundata-exact.R: i Checking if all files are of the same type   > test-filter-immundata-exact.R: v All files have the same extension   > test-filter-immundata-exact.R:   > test-filter-immundata-exact.R: -- Renaming the columns and schemas   > test-filter-immundata-exact.R: v Renaming is finished   > test-filter-immundata-exact.R:   > test-filter-immundata-exact.R: -- Preprocessing the data   > test-filter-immundata-exact.R: 1. exclude_columns   > test-filter-immundata-exact.R: 2. filter_nonproductive   > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column   > test-filter-immundata-exact.R: v Preprocessing plan is ready   > test-filter-immundata-exact.R:   > test-filter-immundata-exact.R: -- Aggregating the data to receptors   > test-filter-immundata-exact.R: i No locus information found   > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R: v 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_28_18_56_34_11186\RtmpYL630M\file899848ab5b62/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899848ab5b62']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.54 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7/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-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7/metadata.json]   > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7]   > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7']   > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c1bd23cc7']   > test-filter-immundata-exact.R:   > test-filter-immundata-exact.R: -- Summary   > test-filter-immundata-exact.R: i Time elapsed: 5.13 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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_28_18_56_34_11186\RtmpYL630M\file8998205b4a42/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998205b4a42']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.55 secs   > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-filter-immundata-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_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70/annotations.parquet]   > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70/metadata.json]   > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70]   > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70']   > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c76e01e70']   > test-filter-immundata-hamm.R:   > test-filter-immundata-hamm.R: -- Summary   > test-filter-immundata-hamm.R: i Time elapsed: 4.91 secs   > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-agg-strata.R: 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-agg-strata.R: i Checking if all files are of the same type   > test-agg-strata.R: v All files have the same extension   > test-agg-strata.R:   > test-agg-strata.R: -- Renaming the columns and schemas   > test-agg-strata.R: v Renaming is finished   > test-agg-strata.R:   > test-agg-strata.R: -- Preprocessing the data   > test-agg-strata.R: 1. exclude_columns   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Reading repertoire data   > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. filter_nonproductive   > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-filter-immundata-lev.R: i Checking if all files are of the same type   > test-filter-immundata-lev.R: v All files have the same extension   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Renaming the columns and schemas   > test-filter-immundata-lev.R: v Renaming is finished   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Preprocessing the data   > test-filter-immundata-lev.R: 1. exclude_columns   > test-filter-immundata-lev.R: 2. filter_nonproductive   > test-agg-strata.R: v Preprocessing plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Aggregating the data to receptors   > test-agg-strata.R: i No locus information found   > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-filter-immundata-lev.R: v Preprocessing plan is ready   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Aggregating the data to receptors   > test-filter-immundata-lev.R: i No locus information found   > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column   > test-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_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31/annotations.parquet]   > test-agg-strata.R: v Joining plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Postprocessing the data   > test-agg-strata.R: 1. prefix_barcodes   > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31/metadata.json]   > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31]   > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31']   > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5de52e31']   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Summary   > test-filter-immundata-lev.R: i Time elapsed: 5.17 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-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_28_18_56_34_11186\RtmpYL630M\file899872206e69/annotations.parquet]   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Reading repertoire data   > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872206e69']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.32 secs   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Renaming the columns and schemas   > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-filter-immundata-lev.R: v Renaming is finished   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Preprocessing the data   > test-filter-immundata-lev.R: 1. exclude_columns   > test-filter-immundata-lev.R: 2. filter_nonproductive   > test-agg-strata.R: 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-agg-strata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-agg-strata.R: i Checking if all files are of the same type   > test-agg-strata.R: v All files have the same extension   > test-filter-immundata-lev.R: v Preprocessing plan is ready   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Aggregating the data to receptors   > test-filter-immundata-lev.R: i No locus information found   > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-agg-strata.R:   > test-agg-strata.R: -- Renaming the columns and schemas   > test-agg-strata.R: v Renaming is finished   > test-agg-strata.R:   > test-agg-strata.R: -- Preprocessing the data   > test-agg-strata.R: 1. exclude_columns   > test-agg-strata.R: 2. filter_nonproductive   > test-agg-strata.R: v Preprocessing plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Aggregating the data to receptors   > test-agg-strata.R: i No locus information found   > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Postprocessing the data   > test-filter-immundata-lev.R: 1. prefix_barcodes   > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-filter-immundata-lev.R: v Postprocessing plan is ready   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk   > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59/annotations.parquet]   > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59/metadata.json]   > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59]   > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59']   > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c5f232b59']   > test-filter-immundata-lev.R:   > test-filter-immundata-lev.R: -- Summary   > test-filter-immundata-lev.R: i Time elapsed: 5.15 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-immundata-regex.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column   > test-filter-immundata-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-agg-strata.R: v Joining plan is ready   > test-agg-strata.R:   > test-agg-strata.R: -- Postprocessing the data   > test-agg-strata.R: 1. prefix_barcodes   > test-filter-immundata-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-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_28_18_56_34_11186\RtmpYL630M\file899869056fd6/annotations.parquet]   > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6/metadata.json]   > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6]   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6']   > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899869056fd6']   > test-agg-strata.R:   > test-agg-strata.R: -- Summary   > test-agg-strata.R: i Time elapsed: 6.77 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-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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-regex.R: v Execution plan for receptor data aggregation and annotation is ready   > test-filter-immundata-regex.R:   > test-filter-immundata-regex.R: -- Postprocessing the data   > test-filter-immundata-regex.R: 1. prefix_barcodes   > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-filter-immundata-regex.R: v Postprocessing plan is ready   > test-filter-immundata-regex.R:   > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk   > test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea/annotations.parquet]   > test-filter-immundata.R: v Preprocessing plan is ready   > test-filter-immundata.R:   > test-filter-immundata.R: -- Aggregating the data to receptors   > test-filter-immundata.R: i No locus information found   > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea/metadata.json]   > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea]   > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea']   > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c39a9dea']   > test-filter-immundata-regex.R:   > test-filter-immundata-regex.R: -- Summary   > test-filter-immundata-regex.R: i Time elapsed: 4.51 secs   > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-filter-receptors.R:   > test-filter-receptors.R: -- Reading repertoire data   > test-filter-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-filter-receptors.R: i Checking if all files are of the same type   > test-filter-receptors.R: v All files have the same extension   > test-filter-receptors.R:   > test-filter-receptors.R: -- Renaming the columns and schemas   > test-filter-receptors.R: v Renaming is finished   > test-filter-receptors.R:   > test-filter-receptors.R: -- Preprocessing the data   > test-filter-receptors.R: 1. exclude_columns   > test-filter-receptors.R: 2. filter_nonproductive   > test-filter-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-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_28_18_56_34_11186\RtmpYL630M\file899872134e4a/annotations.parquet]   > 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_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7/annotations.parquet]   > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a/metadata.json]   > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a]   > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a']   > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899872134e4a']   > test-filter-immundata.R:   > test-filter-immundata.R: -- Summary   > test-filter-immundata.R: i Time elapsed: 6.4 secs   > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-filter-immundata.R:   > test-filter-immundata.R: -- Reading repertoire data   > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-receptors.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7/metadata.json]   > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7]   > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7']   > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c6d22e7']   > test-filter-receptors.R:   > test-filter-receptors.R: -- Summary   > test-filter-receptors.R: i Time elapsed: 5.07 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-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-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-io-immundata.R: v All files have the same extension   > test-io-immundata.R:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-filter-immundata.R: v 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_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.08 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_28_18_56_34_11186\RtmpMVd5Rt\legacy_v1_c35c23e13e4a']   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-io-immundata.R: v All files have the same extension   > test-io-immundata.R:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-filter-immundata.R:   > test-filter-immundata.R: -- Postprocessing the data   > test-filter-immundata.R: 1. prefix_barcodes   > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-filter-immundata.R: v Postprocessing plan is ready   > test-filter-immundata.R:   > test-filter-immundata.R: -- Saving the newly created ImmunData to disk   > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e/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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.18 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-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e/metadata.json]   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e]   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e']   > test-io-immundata.R: v All files have the same extension   > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998502f69e']   > test-filter-immundata.R:   > test-filter-immundata.R: -- Summary   > test-filter-immundata.R: i Time elapsed: 4.95 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:   > 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-stepwise.R:   > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data   > test-io-repertoires-agg-stepwise.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899853667a8e.tsv   > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type   > test-io-repertoires-agg-stepwise.R: v All files have the same extension   > test-io-repertoires-agg-stepwise.R:   > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors   > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only   > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible   > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-agg-stepwise.R:   > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121/annotations.parquet]   > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121/metadata.json]   > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121]   > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121']   > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981bce5121']   > test-io-repertoires-agg-stepwise.R:   > test-io-repertoires-agg-stepwise.R: -- Summary   > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.52 secs   > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]   > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors   Saving _problems/test-io-repertoires-agg-stepwise-125.R   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Reading repertoire data   > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89986e491b03.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_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee/annotations.parquet]   > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee/metadata.json]   > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee]   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee']   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982e9e25ee']   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Summary   > test-io-repertoires-agg.R: i Time elapsed: 0.52 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.29 secs   > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-io-immundata.R: v All files have the same extension   > test-io-immundata.R:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Reading repertoire data   > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998325a1c69.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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 1.82 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: Rows: 2 Columns: 4   > test-io-immundata.R: -- Column specification --------------------------------------------------------   > test-io-immundata.R: Delimiter: "\t"   > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix   > test-io-immundata.R:   > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data.   > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.   > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk   > test-io-immundata.R: v Metadata parsed successfully   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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: 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_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec/annotations.parquet]   > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec/metadata.json]   > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec]   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec']   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d4012ec']   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Summary   > test-io-repertoires-agg.R: i Time elapsed: 2.36 secs   > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]   > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Reading repertoire data   > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89983bcc170f.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-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_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07/annotations.parquet]   > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07/metadata.json]   > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07]   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07']   > 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-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899843625b07']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Summary   > test-io-repertoires-agg.R: i Time elapsed: 2.65 secs   > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]   > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Reading repertoire data   > test-io-repertoires-agg.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file899816365064.tsv   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > 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: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 4.97 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-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: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\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_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.05 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002']   > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177/metadata.json]   > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177]   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177']   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983d6177']   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\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:   > test-io-repertoires-agg.R: -- Summary   > test-io-repertoires-agg.R: i Time elapsed: 2.46 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 [4] chains and [2] receptors   > 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_28_18_56_34_11186\RtmpYL630M\file899813ad46f6.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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 1.93 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\treated\v001']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB']   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-io-immundata.R: v All files have the same extension   > test-io-immundata.R:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-repertoires-agg.R: 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_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197/annotations.parquet]   > test-io-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197/metadata.json]   > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197]   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197']   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899817d34197']   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Summary   > test-io-repertoires-agg.R: i Time elapsed: 2.37 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_28_18_56_34_11186\RtmpYL630M\file8998bd650a0.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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.2 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v002']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\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_28_18_56_34_11186\RtmpMVd5Rt\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\CRANpkg\lib\4.5\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: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Postprocessing the data   > test-io-repertoires-agg.R: 1. prefix_barcodes   > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-io-repertoires-agg.R: v Postprocessing plan is ready   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7/annotations.parquet]   > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7/metadata.json]   > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7]   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7']   > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987cb263b7']   > test-io-repertoires-agg.R:   > test-io-repertoires-agg.R: -- Summary   > test-io-repertoires-agg.R: i Time elapsed: 2.36 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   Saving _problems/test-io-repertoires-agg-47.R   Saving _problems/test-io-repertoires-agg-47.R   Saving _problems/test-io-repertoires-agg-47.R   Saving _problems/test-io-repertoires-agg-64.R   Saving _problems/test-io-repertoires-agg-70.R   Saving _problems/test-io-repertoires-agg-88.R   Saving _problems/test-io-repertoires-agg-96.R   > 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Reading repertoire data   > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998655a686f.tsv   > test-io-repertoires-counts.R: i Checking if all files are of the same type   > test-io-repertoires-counts.R: v All files have the same extension   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Aggregating the data to receptors   > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only   > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.01 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001']   > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba/annotations.parquet]   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89981da24eba']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 0.55 secs   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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_28_18_56_34_11186\RtmpYL630M\file8998d8c7465.tsv   > test-io-repertoires-counts.R: i Checking if all files are of the same type   > test-io-repertoires-counts.R: v All files have the same extension   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Aggregating the data to receptors   > test-io-immundata.R:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only   > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible   > test-io-immundata.R: 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_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1/annotations.parquet]   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899845025be1']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 0.54 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_28_18_56_34_11186\RtmpYL630M\file89987b449c2.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 Preprocessing plan is ready   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0/annotations.parquet]   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899870d420a0']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 2.16 secs   > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]   > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Reading repertoire data   > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file8998696d8b2.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_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e/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_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c2db2656e']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 4.85 secs   > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899823e45d9f']   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-immundata.R: v All files have the same extension   > test-io-repertoires-counts.R: i Time elapsed: 2.08 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:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Reading repertoire data   > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89983e73671a.tsv   > test-io-repertoires-counts.R: i Checking if all files are of the same type   > test-io-repertoires-counts.R: v All files have the same extension   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Aggregating the data to receptors   > test-io-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-counts.R: i 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_28_18_56_34_11186\RtmpMVd5Rt\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_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 1.85 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_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\baseline\v001']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB']   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001]   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectB\snapshots\baseline\v001']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899844032725']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-counts.R: i Time elapsed: 2.11 secs   > 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: 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:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Reading repertoire data   > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89984843548e.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-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.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 Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only   > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible   > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk   > test-io-immundata.R:   > test-io-immundata.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f/annotations.parquet]   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 2.52 secs   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f]   > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f']   > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89987585f7f']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 2.4 secs   > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")]   > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors   > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet]   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Reading repertoire data   > test-io-repertoires-counts.R: 1. D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\file89983c673350.tsv   > test-io-repertoires-counts.R: i Checking if all files are of the same type   > test-io-repertoires-counts.R: v All files have the same extension   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Aggregating the data to receptors   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\imd_snap_tests\projectA\snapshots\ops\v001]   > 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-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920/annotations.parquet]   > 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_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984fe41920']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 0.3 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_28_18_56_34_11186\RtmpYL630M\file89986ab36b31.tsv   > test-io-repertoires-counts.R: i Checking if all files are of the same type   > test-io-immundata.R: v Renaming is finished   > test-io-immundata.R:   > test-io-immundata.R: -- Preprocessing the data   > test-io-repertoires-counts.R: v All files have the same extension   > test-io-immundata.R: 1. exclude_columns   > 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: 2. filter_nonproductive   > test-io-immundata.R: v Preprocessing plan is ready   > test-io-immundata.R:   > test-io-immundata.R: -- Aggregating the data to receptors   > test-io-immundata.R: i No locus information found   > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e/annotations.parquet]   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e/metadata.json]   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e']   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998511295e']   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 2.26 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_28_18_56_34_11186\RtmpYL630M\file89986ab36b31.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_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd/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_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c66af48dd']   > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b/metadata.json]   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 5.12 secs   > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b']   > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871cd5c3b']   > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-io-repertoires-counts.R:   > test-io-repertoires-counts.R: -- Summary   > test-io-repertoires-counts.R: i Time elapsed: 2.59 secs   > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")]   > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors   > test-io-immundata.R:   > test-io-immundata.R: -- Reading repertoire data   > test-io-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-io-immundata.R: i Checking if all files are of the same type   > test-io-immundata.R: v All files have the same extension   > test-io-immundata.R:   > test-io-immundata.R: -- Renaming the columns and schemas   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Reading repertoire data   > test-io-repertoires-files.R: 1. D:\RCompile\CRANpkg\lib\4.5\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-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-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: 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-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_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07/annotations.parquet]   > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07/metadata.json]   > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07]   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07']   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899871252f07']   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Summary   > test-io-repertoires-files.R: i Time elapsed: 2.27 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e/annotations.parquet]   > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e/metadata.json]   > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e]   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e']   > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\filec35c52275d9e']   > test-io-immundata.R:   > test-io-immundata.R: -- Summary   > test-io-immundata.R: i Time elapsed: 4.87 secs   > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Reading repertoire data   > test-io-repertoires-processing.R: 1. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19/annotations.parquet]   > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19/metadata.json]   > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19]   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19']   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89982af62e19']   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Summary   > test-io-repertoires-files.R: i Time elapsed: 3.98 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\test-exclude/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude/metadata.json]   > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude]   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude']   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude']   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Summary   > test-io-repertoires-processing.R: i Time elapsed: 2.21 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-processing.R: i Checking if all files are of the same type   > test-io-repertoires-processing.R: v All files have the same extension   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Renaming the columns and schemas   > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene   > test-io-repertoires-processing.R: v Renaming is finished   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Preprocessing the data   > test-io-repertoires-processing.R: 1. exclude_columns   > test-io-repertoires-processing.R: 2. filter_nonproductive   > test-io-repertoires-processing.R: v Preprocessing plan is ready   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Aggregating the data to receptors   > test-io-repertoires-processing.R: i No locus information found   > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Postprocessing the data   > test-io-repertoires-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-processing.R: 1. prefix_barcodes   > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing   > test-io-repertoires-processing.R: v Postprocessing plan is ready   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename/metadata.json]   > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename]   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename']   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-rename']   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Summary   > test-io-repertoires-processing.R: i Time elapsed: 2.72 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. D:\RCompile\CRANpkg\lib\4.5\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: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a/metadata.json]   > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a]   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a']   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89986d7e309a']   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Summary   > test-io-repertoires-files.R: i Time elapsed: 3.84 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename/metadata.json]   > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename]   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename']   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-exclude-rename']   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Summary   > test-io-repertoires-processing.R: i Time elapsed: 2.18 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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json]   > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k]   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k']   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\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: 2.96 secs   > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors   > test-io-repertoires-files.R: 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_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2/annotations.parquet]   > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2/metadata.json]   > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2]   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2']   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89984466fe2']   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Summary   > test-io-repertoires-files.R: i Time elapsed: 5.45 secs   > test-io-repertoires-processing.R: Rows: 1000 Columns: 40   > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]   > 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-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors   > 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\CRANpkg\lib\4.5\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: 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-processing.R:   > test-io-repertoires-processing.R: -- Renaming the columns and schemas   > 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-io-repertoires-files.R: i Checking if all files are of the same type   > test-io-repertoires-files.R: v All files have the same extension   > test-io-repertoires-processing.R: v 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:   > 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\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json]   > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k]   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\immundata-sample_0_1k']   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANpkg\lib\4.5\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: 2.29 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-processing.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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:   > 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 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_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4/annotations.parquet]   > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4/metadata.json]   > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4]   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4']   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899837e43df4']   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Summary   > test-io-repertoires-files.R: i Time elapsed: 5.25 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\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv   > test-io-repertoires-files.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv   > test-io-repertoires-files.R: i Checking if all files are of the same type   > test-io-repertoires-files.R: v All files have the same extension   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Renaming the columns and schemas   > test-io-repertoires-files.R: v Renaming is finished   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Aggregating the data to receptors   > test-io-repertoires-files.R: i No locus information found   > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible   > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column   > test-io-repertoires-processing.R: v Joining plan is ready   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Aggregating repertoires...   > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column   > test-io-repertoires-files.R: v Joining plan is ready   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk   > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1/annotations.parquet]   > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1/metadata.json]   > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1]   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1']   > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_8998118276f1']   > test-io-repertoires-files.R:   > test-io-repertoires-files.R: -- Summary   > test-io-repertoires-files.R: i Time elapsed: 5.23 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. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96/annotations.parquet]   > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96/metadata.json]   > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96]   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96']   > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35cb184f96']   > test-io-repertoires-processing.R:   > test-io-repertoires-processing.R: -- Summary   > test-io-repertoires-processing.R: i Time elapsed: 32.99 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. D:\RCompile\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8/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_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4/annotations.parquet]   > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4/metadata.json]   > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4]   > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4']   > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c6e846e4']   > test-io-repertoires-schema-single.R:   > test-io-repertoires-schema-single.R: -- Summary   > test-io-repertoires-schema-single.R: i Time elapsed: 5.63 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_28_18_56_34_11186\RtmpMVd5Rt\filec35c4fe1227b.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_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958/annotations.parquet]   > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958/metadata.json]   > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958]   > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958']   > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c58061958']   > test-io-repertoires-schema-single.R:   > test-io-repertoires-schema-single.R: -- Summary   > test-io-repertoires-schema-single.R: i Time elapsed: 0.44 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_28_18_56_34_11186\RtmpMVd5Rt\filec35c232264c2.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_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24/annotations.parquet]   > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24/metadata.json]   > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24]   > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24']   > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test_immundata_c35c1e5aa24']   > test-io-repertoires-schema-single.R:   > test-io-repertoires-schema-single.R: -- Summary   > test-io-repertoires-schema-single.R: i Time elapsed: 0.42 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\CRANpkg\lib\4.5\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-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8/metadata.json]   > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8]   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8']   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899857a677f8']   > test-io-repertoires-schema-paired.R:   > test-io-repertoires-schema-paired.R: -- Summary   > test-io-repertoires-schema-paired.R: i Time elapsed: 34.61 secs   > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")]   > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors   > test-io-repertoires-schema-paired.R:   > test-io-repertoires-schema-paired.R: -- Reading repertoire data   > test-io-repertoires-schema-paired.R: 1. D:\RCompile\CRANpkg\lib\4.5\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 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-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_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes/annotations.parquet]   > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes/metadata.json]   > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes]   > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\test-no-barcodes']   > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpMVd5Rt\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: 2.52 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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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\CRANpkg\lib\4.5\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_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6/annotations.parquet]   > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6/metadata.json]   > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6]   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6']   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_899899220a6']   > test-io-repertoires-schema-paired.R:   > test-io-repertoires-schema-paired.R: -- Summary   > test-io-repertoires-schema-paired.R: i Time elapsed: 34.09 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_28_18_56_34_11186\RtmpYL630M\file8998589812da.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_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0/annotations.parquet]   > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0/metadata.json]   > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0]   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0']   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89985e222b0']   > test-io-repertoires-schema-paired.R:   > test-io-repertoires-schema-paired.R: -- Summary   > test-io-repertoires-schema-paired.R: i Time elapsed: 2.33 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_28_18_56_34_11186\RtmpYL630M\file899865fe5857.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_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81/annotations.parquet]   > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81/metadata.json]   > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81]   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81']   > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_28_18_56_34_11186\RtmpYL630M\test_immundata_89983ae75c81']   > test-io-repertoires-schema-paired.R:   > test-io-repertoires-schema-paired.R: -- Summary   > test-io-repertoires-schema-paired.R: i Time elapsed: 2.32 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 8 | WARN 0 | SKIP 0 | PASS 316 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ──   <duckdb_error/rlang_error/error/condition>   Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL) { fields <- list() fields$context <- context fields$error_type <- error_type fields$raw_message <- raw_message fields$extra_info <- extra_info error_parts <- c(message, i = paste0("Context: ", context)) if (!is.null(error_type)) { error_parts <- c(error_parts, i = paste0("Error type: ", error_type)) } if (length(extra_info) > 0) { info_text <- paste0(names(extra_info), ": ", extra_info) names(info_text) <- rep_len("i", length(info_text)) error_parts <- c(error_parts, info_text) } rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER)   This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.   For more information, see https://duckdb.org/docs/stable/dev/internal_errors   i Context: GetQueryResult   Backtrace:        ▆     1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3     2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations)     3. │ ├─dplyr::collect(out)     4. │ └─duckplyr:::collect.duckplyr_df(out)     5. │ └─base::nrow(x)     6. │ ├─base::dim(x)     7. │ └─base::dim.data.frame(x)     8. │ └─base::.row_names_info(x, 2L)     9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")    10. └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)   ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `all(ann_na_counts == 0)` to be TRUE.   Differences:   `actual`: FALSE   `expected`: TRUE      context: single-chain duplicated receptors   agg schema: sample_id   input annotation shape: 5x13   input repertoire shape: <not captured>   annotation shape: 5x16   repertoire shape: 2x4   missing annotation columns: <none>   missing repertoire columns: <none>   annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0   repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2   unmatched repertoire ids: NA      input annotations dump:    cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count    cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 0    cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 0    cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 0    cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 0    cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 0      input repertoires dump:   <NULL>      annotations dump:    cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires    cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 NA NA NA 1    cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 NA NA NA 1    cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 NA NA NA 1    cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 NA NA NA 1    cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 NA NA NA 1      repertoires dump:    imd_repertoire_id sample_id n_barcodes n_receptors    1 Sample2 2 NA    2 Sample1 3 NA   Backtrace:       ▆    1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3    2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3    3. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5   ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `all(reps_na_counts == 0)` to be TRUE.   Differences:   `actual`: FALSE   `expected`: TRUE      context: single-chain duplicated receptors   agg schema: sample_id   input annotation shape: 5x13   input repertoire shape: <not captured>   annotation shape: 5x16   repertoire shape: 2x4   missing annotation columns: <none>   missing repertoire columns: <none>   annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0   repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2   unmatched repertoire ids: NA      input annotations dump:    cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count    cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 0    cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 0    cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 0    cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 0    cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 0      input repertoires dump:   <NULL>      annotations dump:    cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires    cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 NA NA NA 1    cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 NA NA NA 1    cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 NA NA NA 1    cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 NA NA NA 1    cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 NA NA NA 1      repertoires dump:    imd_repertoire_id sample_id n_barcodes n_receptors    1 Sample2 2 NA    2 Sample1 3 NA   Backtrace:       ▆    1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3    2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3    3. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5   ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `nrow(unmatched_repertoire_ids)` to equal 0.   Differences:     `actual`: 1.0   `expected`: 0.0      context: single-chain duplicated receptors   agg schema: sample_id   input annotation shape: 5x13   input repertoire shape: <not captured>   annotation shape: 5x16   repertoire shape: 2x4   missing annotation columns: <none>   missing repertoire columns: <none>   annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0   repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2   unmatched repertoire ids: NA      input annotations dump:    cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count    cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 0    cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 0    cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 0    cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 0    cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 0      input repertoires dump:   <NULL>      annotations dump:    cell_id sample_id v_call j_call junction_aa locus umi_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires    cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell1 1 3 1 NA NA NA 1    cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell2 2 3 1 NA NA NA 1    cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell3 3 4 1 NA NA NA 1    cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell4 4 2 1 NA NA NA 1    cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_28_18_56_34_11186\\RtmpYL630M\\file89986e491b03.tsv cell5 5 1 1 NA NA NA 1      repertoires dump:    imd_repertoire_id sample_id n_barcodes n_receptors    1 Sample2 2 NA    2 Sample1 3 NA   Backtrace:       ▆    1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3    2. └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3    3. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5   ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `sample1_stats$n_receptors` to equal 2.   Differences:     `actual`: NA   `expected`: 2.0      Sample1 should have 2 unique receptors   ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `sample2_stats$n_receptors` to equal 2.   Differences:     `actual`: NA   `expected`: 2.0      Sample2 should have 2 unique receptors   ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `sample1_counts$total_count1[1]` to equal 2.   Differences:     `actual`: NA   `expected`: 2.0      Shared receptor should have count of 2   ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ──   Expected `sample1_counts$total_count2[1]` to equal 2.   Differences:     `actual`: NA   `expected`: 2.0      Shared receptor should have count of 2      [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [21s] OK
• checking HTML version of manual ... [7s] OK
• DONE

Status: 1 ERROR