R Under development (unstable) (2026-03-14 r89623 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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: 10. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07ae94ed8/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07ae94ed8/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07ae94ed8] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07ae94ed8'] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07ae94ed8'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 2.65 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104ee06ef3/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104ee06ef3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104ee06ef3] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104ee06ef3'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104ee06ef3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.4 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51035d049d7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51035d049d7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51035d049d7] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51035d049d7'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51035d049d7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.58 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a070b456bb/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a070b456bb/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a070b456bb] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a070b456bb'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a070b456bb'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.68 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51029d81243/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-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51029d81243/metadata.json] > test-annotate-external.R: 1. prefix_barcodes > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51029d81243] > 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: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51029d81243'] > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a06ae05880/annotations.parquet] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51029d81243'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a06ae05880/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a06ae05880] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a06ae05880'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a06ae05880'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.98 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: 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: -- Renaming the columns and schemas > test-annotate-external.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-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_15_23_35_17_2377\RtmpgffA4V\file8a07e836bf7/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_15_23_35_17_2377\RtmpgffA4V\file8a07e836bf7/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07e836bf7] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07e836bf7'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07e836bf7'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.99 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-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_15_23_35_17_2377\RtmpaI1emF\filea51074f753e/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_15_23_35_17_2377\RtmpaI1emF\filea51074f753e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51074f753e] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51074f753e'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51074f753e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.87 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a066c74569/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a066c74569/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a066c74569] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a066c74569'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a066c74569'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.07 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51037481cac/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51037481cac/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51037481cac] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51037481cac'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51037481cac'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.88 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07d61115b/annotations.parquet] > 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_15_23_35_17_2377\RtmpgffA4V\file8a07d61115b/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07d61115b] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07d61115b'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07d61115b'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.98 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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: -- Reading repertoire data > test-annotate-receptors.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106e171b7d/annotations.parquet] > 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_15_23_35_17_2377\RtmpgffA4V\file8a073361c77/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106e171b7d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106e171b7d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106e171b7d'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106e171b7d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.75 secs > test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a073361c77/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a073361c77] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a073361c77'] > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a073361c77'] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 2.99 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03d7270e7/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03d7270e7/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03d7270e7] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03d7270e7'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03d7270e7'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.85 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5107f773c1f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5107f773c1f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5107f773c1f] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5107f773c1f'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5107f773c1f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.82 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0718117b5/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0718117b5/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0718117b5] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0718117b5'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0718117b5'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.91 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-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 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-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0671a7cd/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0671a7cd/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0671a7cd] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0671a7cd'] > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0671a7cd'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.83 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104b5b6745/annotations.parquet] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104b5b6745/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104b5b6745] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104b5b6745'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104b5b6745'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.85 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 Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a029663b55/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_15_23_35_17_2377\RtmpgffA4V\file8a029663b55/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a029663b55] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a029663b55'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a029663b55'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.8 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03a1743a3.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05bf4d3a/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05bf4d3a/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05bf4d3a] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05bf4d3a'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05bf4d3a'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.35 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [8] chains and [8] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106dd9717e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106dd9717e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106dd9717e] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106dd9717e'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106dd9717e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.9 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03292e7f.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a04a295cc7/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a04a295cc7/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a04a295cc7] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a04a295cc7'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a04a295cc7'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.15 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL] > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0569f176c.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a0977499f/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a0977499f/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a0977499f] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a0977499f'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a0977499f'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 1.47 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-downsample.R: v Loaded ImmunData with [12] chains and [6] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106d5379a/annotations.parquet] > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. > test-downsample.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106d5379a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106d5379a] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106d5379a'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106d5379a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.99 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5105cbb32ed/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5105cbb32ed/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5105cbb32ed] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5105cbb32ed'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5105cbb32ed'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.8 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51052123537/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51052123537/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51052123537] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51052123537'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51052123537'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.79 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510e64d3e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510e64d3e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510e64d3e] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510e64d3e'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510e64d3e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.77 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103b376643/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103b376643/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103b376643] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103b376643'] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103b376643'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 2.94 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01dd06278/annotations.parquet] > 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-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103df473ac/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103df473ac/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103df473ac] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103df473ac'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103df473ac'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 2.97 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01dd06278/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01dd06278] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01dd06278'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01dd06278'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 21.41 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-downsample.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a067b04f85.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51064286d21/annotations.parquet] > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a06de86ba2/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a06de86ba2/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a06de86ba2] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a06de86ba2'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a06de86ba2'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.33 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [8] chains and [6] receptors > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51064286d21/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51064286d21] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51064286d21'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51064286d21'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.49 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-downsample.R: 2. > test-downsample.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Renaming the columns and schemas > test-downsample.R: v Renaming is finished > test-downsample.R: > test-downsample.R: -- Preprocessing the data > test-downsample.R: 1. exclude_columns > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-downsample.R: 2. filter_nonproductive > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-downsample.R: v Preprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Postprocessing the data > test-downsample.R: 1. prefix_barcodes > test-downsample.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-downsample.R: v Postprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07b336dda/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51043654a8f/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07b336dda/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07b336dda] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07b336dda'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a07b336dda'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 2.99 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-downsample.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a016ce200d.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51043654a8f/metadata.json] > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51043654a8f] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51043654a8f'] > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51043654a8f'] > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 2.98 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a037286e82/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a037286e82/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a037286e82] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a037286e82'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a037286e82'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.37 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [6] chains and [6] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a04a16560.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05f94369e/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05f94369e/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05f94369e] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05f94369e'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a05f94369e'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.17 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL] > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a03c2a671a.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a054013919/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a054013919/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a054013919] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a054013919'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a054013919'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.15 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL] > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51045a44d8c/annotations.parquet] > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-downsample.R: 2. > test-downsample.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Renaming the columns and schemas > test-downsample.R: v Renaming is finished > test-downsample.R: > test-downsample.R: -- Preprocessing the data > test-downsample.R: 1. exclude_columns > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51045a44d8c/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51045a44d8c] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51045a44d8c'] > test-downsample.R: 2. filter_nonproductive > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51045a44d8c'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.16 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-downsample.R: v Preprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-filter-immundata-regex.R: > test-downsample.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Postprocessing the data > test-downsample.R: 1. prefix_barcodes > test-downsample.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-downsample.R: v Postprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a078092b37/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a078092b37/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a078092b37] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a078092b37'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a078092b37'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 2.97 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-downsample.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a04462ee3.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-filter-immundata-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_15_23_35_17_2377\RtmpaI1emF\filea510624e10e0/annotations.parquet] > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01c1ddf6/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01c1ddf6/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01c1ddf6] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01c1ddf6'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a01c1ddf6'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.32 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [6] chains and [4] receptors > test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510624e10e0/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510624e10e0] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510624e10e0'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510624e10e0'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 2.99 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive Saving _problems/test-downsample-37.R Saving _problems/test-downsample-37.R Saving _problems/test-downsample-37.R Saving _problems/test-downsample-39.R Saving _problems/test-downsample-89.R Saving _problems/test-downsample-89.R Saving _problems/test-downsample-89.R Saving _problems/test-downsample-91.R Saving _problems/test-downsample-234.R Saving _problems/test-downsample-234.R Saving _problems/test-downsample-234.R Saving _problems/test-downsample-236.R Saving _problems/test-downsample-326.R Saving _problems/test-downsample-326.R Saving _problems/test-downsample-326.R Saving _problems/test-downsample-336.R Saving _problems/test-downsample-374.R Saving _problems/test-downsample-374.R Saving _problems/test-downsample-374.R Saving _problems/test-downsample-376.R Saving _problems/test-downsample-411.R Saving _problems/test-downsample-411.R Saving _problems/test-downsample-411.R Saving _problems/test-downsample-413.R Saving _problems/test-downsample-470.R Saving _problems/test-downsample-470.R Saving _problems/test-downsample-470.R Saving _problems/test-downsample-472.R > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a064794763/annotations.parquet] > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a064794763/metadata.json] > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a064794763] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a064794763'] > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51055291454/annotations.parquet] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a064794763'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 2.97 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51055291454/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51055291454] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51055291454'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51055291454'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.89 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\legacy_v1_8a09ff1487/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\legacy_v1_8a09ff1487/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\legacy_v1_8a09ff1487] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\legacy_v1_8a09ff1487'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\legacy_v1_8a09ff1487'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.31 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\legacy_v1_8a09ff1487'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.31 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > 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: 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_15_23_35_17_2377\RtmpaI1emF\filea51012cb120a/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51012cb120a/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51012cb120a] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51012cb120a'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51012cb120a'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 2.96 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104e2c4e26.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51051eb2325/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51051eb2325/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51051eb2325] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51051eb2325'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51051eb2325'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.33 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.39 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51063792414.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.39 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105cee2f09/annotations.parquet] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105cee2f09/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105cee2f09] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105cee2f09'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105cee2f09'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.42 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [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_15_23_35_17_2377\RtmpaI1emF\filea51072d428cc.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51010f61ba2/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51010f61ba2/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51010f61ba2] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51010f61ba2'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51010f61ba2'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.38 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-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51067b1141c.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: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.28 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105514231b/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105514231b/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105514231b] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105514231b'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105514231b'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.92 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-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.4 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5106fd622d.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068f17d2d/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.38 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068f17d2d/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068f17d2d] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068f17d2d'] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068f17d2d'] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\treated\v001] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\treated\v001'] > test-io-repertoires-agg.R: i Time elapsed: 1.41 secs > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB/annotations.parquet] > 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_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104794f6f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.37 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510305e3fbb/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510305e3fbb/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510305e3fbb] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510305e3fbb'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510305e3fbb'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.5 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-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510b565a17.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: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51064564c7c/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51064564c7c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51064564c7c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51064564c7c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51064564c7c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.33 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5102a9979e4.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_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.41 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\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_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51092b2a47/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51092b2a47/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51092b2a47] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51092b2a47'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51092b2a47'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-counts.R: i Time elapsed: 0.32 secs > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea51016864859.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510f707863/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510f707863/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510f707863] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510f707863'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510f707863'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.43 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_15_23_35_17_2377\RtmpaI1emF\filea5102d1d53dc.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-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105f0d7169/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a085d1ada/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105f0d7169/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105f0d7169] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105f0d7169'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5105f0d7169'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.32 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510587a7161.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a085d1ada/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a085d1ada] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a085d1ada'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a085d1ada'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.08 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 [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024b493f/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.38 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024b493f/metadata.json] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB/annotations.parquet] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024b493f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024b493f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024b493f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB/metadata.json] > test-io-repertoires-counts.R: i Time elapsed: 1.87 secs > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB] > 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: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectB\snapshots\baseline\v001'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103d233d93.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: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i 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 Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5108b27766/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.37 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\ops\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\imd_snap_tests\projectA\snapshots\ops\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5108b27766/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5108b27766] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5108b27766'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5108b27766'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.9 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5102eee2c0a.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068b5134a/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068b5134a/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068b5134a] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068b5134a'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51068b5134a'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.16 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510333e4420.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_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106bb949ba/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106bb949ba/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106bb949ba] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106bb949ba'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106bb949ba'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.44 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea510333e4420.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a09db45e5/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a09db45e5/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a09db45e5] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a09db45e5'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a09db45e5'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.08 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 [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51032ad7b24/annotations.parquet] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51032ad7b24/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51032ad7b24] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51032ad7b24'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51032ad7b24'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.51 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510239861d2/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510239861d2/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510239861d2] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510239861d2'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510239861d2'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.32 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0110b4bae/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0110b4bae/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0110b4bae] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0110b4bae'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a0110b4bae'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.06 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510460ff35/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510460ff35/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510460ff35] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510460ff35'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510460ff35'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.47 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.38 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > 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 Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > 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-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: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.69 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106e2b38c4/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106e2b38c4/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106e2b38c4] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106e2b38c4'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5106e2b38c4'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.42 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.41 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.66 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_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510416618bc/annotations.parquet] > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510416618bc/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510416618bc] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510416618bc'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a510416618bc'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.19 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.36 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: Rows: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5103293499/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5103293499/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5103293499] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5103293499'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5103293499'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.07 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104d637225/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104d637225/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104d637225] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104d637225'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104d637225'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.05 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a072d42aa4/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a072d42aa4/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a072d42aa4] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a072d42aa4'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a072d42aa4'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 19.23 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104bd252c6/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a08fa1407/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a08fa1407/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a08fa1407] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a08fa1407'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a08fa1407'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 3.52 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a054df7b71.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a07cc3eb0/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a07cc3eb0/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a07cc3eb0] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a07cc3eb0'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a07cc3eb0'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.32 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\file8a039ef773b.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a09e6b72/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a09e6b72/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a09e6b72] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a09e6b72'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test_immundata_8a09e6b72'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.33 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104bd252c6/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104bd252c6] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104bd252c6'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a5104bd252c6'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 21.2 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-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpgffA4V\test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 1.86 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-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51048827df0/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51048827df0/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51048827df0] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51048827df0'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51048827df0'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 21.3 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5104366545b.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024ce2db1/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024ce2db1/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024ce2db1] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024ce2db1'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51024ce2db1'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.23 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\filea5103a866eb5.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51077791f60/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51077791f60/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51077791f60] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51077791f60'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_35_17_2377\RtmpaI1emF\test_immundata_a51077791f60'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.3 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 35 | WARN 0 | SKIP 0 | PASS 358 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-downsample.R:33:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample single-cell deterministic agg schema: sample_id input annotation shape: 8x13 input repertoire shape: annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, 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 c1 S1 IGHV1 IGHJ1 CARA IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c1 1 4 1 0 c2 S1 IGHV2 IGHJ2 CARB IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c2 2 5 1 0 c3 S1 IGHV3 IGHJ3 CARC IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c3 3 1 1 0 c4 S1 IGHV4 IGHJ4 CARD IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c4 4 3 1 0 c5 S2 IGHV1 IGHJ1 CARE IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c5 5 8 1 0 c6 S2 IGHV2 IGHJ2 CARF IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c6 6 2 1 0 c7 S2 IGHV3 IGHJ3 CARG IGH 16 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c7 7 6 1 0 c8 S2 IGHV4 IGHJ4 CARH IGH 17 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c8 8 7 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 CARA IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c1 1 4 1 NA NA NA 1 c2 S1 IGHV2 IGHJ2 CARB IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c2 2 5 1 NA NA NA 1 c3 S1 IGHV3 IGHJ3 CARC IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c3 3 1 1 NA NA NA 1 c4 S1 IGHV4 IGHJ4 CARD IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c4 4 3 1 NA NA NA 1 c5 S2 IGHV1 IGHJ1 CARE IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c5 5 8 1 NA NA NA 1 c6 S2 IGHV2 IGHJ2 CARF IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c6 6 2 1 NA NA NA 1 c7 S2 IGHV3 IGHJ3 CARG IGH 16 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c7 7 6 1 NA NA NA 1 c8 S2 IGHV4 IGHJ4 CARH IGH 17 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c8 8 7 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 4 NA 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:33:3 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-downsample.R:33:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample single-cell deterministic agg schema: sample_id input annotation shape: 8x13 input repertoire shape: annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, 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 c1 S1 IGHV1 IGHJ1 CARA IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c1 1 4 1 0 c2 S1 IGHV2 IGHJ2 CARB IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c2 2 5 1 0 c3 S1 IGHV3 IGHJ3 CARC IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c3 3 1 1 0 c4 S1 IGHV4 IGHJ4 CARD IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c4 4 3 1 0 c5 S2 IGHV1 IGHJ1 CARE IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c5 5 8 1 0 c6 S2 IGHV2 IGHJ2 CARF IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c6 6 2 1 0 c7 S2 IGHV3 IGHJ3 CARG IGH 16 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c7 7 6 1 0 c8 S2 IGHV4 IGHJ4 CARH IGH 17 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c8 8 7 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 CARA IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c1 1 4 1 NA NA NA 1 c2 S1 IGHV2 IGHJ2 CARB IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c2 2 5 1 NA NA NA 1 c3 S1 IGHV3 IGHJ3 CARC IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c3 3 1 1 NA NA NA 1 c4 S1 IGHV4 IGHJ4 CARD IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c4 4 3 1 NA NA NA 1 c5 S2 IGHV1 IGHJ1 CARE IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c5 5 8 1 NA NA NA 1 c6 S2 IGHV2 IGHJ2 CARF IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c6 6 2 1 NA NA NA 1 c7 S2 IGHV3 IGHJ3 CARG IGH 16 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c7 7 6 1 NA NA NA 1 c8 S2 IGHV4 IGHJ4 CARH IGH 17 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c8 8 7 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 4 NA 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:33:3 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-downsample.R:33:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample single-cell deterministic agg schema: sample_id input annotation shape: 8x13 input repertoire shape: annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, 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 c1 S1 IGHV1 IGHJ1 CARA IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c1 1 4 1 0 c2 S1 IGHV2 IGHJ2 CARB IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c2 2 5 1 0 c3 S1 IGHV3 IGHJ3 CARC IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c3 3 1 1 0 c4 S1 IGHV4 IGHJ4 CARD IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c4 4 3 1 0 c5 S2 IGHV1 IGHJ1 CARE IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c5 5 8 1 0 c6 S2 IGHV2 IGHJ2 CARF IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c6 6 2 1 0 c7 S2 IGHV3 IGHJ3 CARG IGH 16 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c7 7 6 1 0 c8 S2 IGHV4 IGHJ4 CARH IGH 17 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c8 8 7 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 CARA IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c1 1 4 1 NA NA NA 1 c2 S1 IGHV2 IGHJ2 CARB IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c2 2 5 1 NA NA NA 1 c3 S1 IGHV3 IGHJ3 CARC IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c3 3 1 1 NA NA NA 1 c4 S1 IGHV4 IGHJ4 CARD IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c4 4 3 1 NA NA NA 1 c5 S2 IGHV1 IGHJ1 CARE IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c5 5 8 1 NA NA NA 1 c6 S2 IGHV2 IGHJ2 CARF IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c6 6 2 1 NA NA NA 1 c7 S2 IGHV3 IGHJ3 CARG IGH 16 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c7 7 6 1 NA NA NA 1 c8 S2 IGHV4 IGHJ4 CARH IGH 17 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03a1743a3.tsv c8 8 7 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 4 NA 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:33:3 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 ── Error ('test-downsample.R:39:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Error in `downsample_immundata(idata, n = 2, seed = 100)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 2, seed = 100) at test-downsample.R:39:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:85:3'): downsample_immundata downsampled bulk repertoires by count ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample bulk count mode agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:85:3 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-downsample.R:85:3'): downsample_immundata downsampled bulk repertoires by count ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample bulk count mode agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:85:3 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-downsample.R:85:3'): downsample_immundata downsampled bulk repertoires by count ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample bulk count mode agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03292e7f.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:85:3 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 ── Error ('test-downsample.R:91:3'): downsample_immundata downsampled bulk repertoires by count ── Error in `downsample_immundata(idata, n = 5, seed = 42)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 5, seed = 42) at test-downsample.R:91:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:230:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n=1 receptor mode agg schema: sample_id input annotation shape: 8x13 input repertoire shape: annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, 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 s1c1 S1 IGHV1 IGHJ1 A IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c1 1 3 1 0 s1c2 S1 IGHV1 IGHJ1 A IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c2 2 3 1 0 s1c3 S1 IGHV2 IGHJ2 B IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c3 3 1 1 0 s1c4 S1 IGHV3 IGHJ3 C IGH 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c4 4 4 1 0 s2c1 S2 IGHV4 IGHJ4 D IGH 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c1 5 6 1 0 s2c2 S2 IGHV5 IGHJ5 E IGH 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c2 6 5 1 0 s2c3 S2 IGHV5 IGHJ5 E IGH 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c3 7 5 1 0 s2c4 S2 IGHV6 IGHJ6 F IGH 5 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c4 8 2 1 0 input repertoires dump: 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 s1c1 S1 IGHV1 IGHJ1 A IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c1 1 3 1 NA NA NA 1 s1c2 S1 IGHV1 IGHJ1 A IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c2 2 3 1 NA NA NA 1 s1c3 S1 IGHV2 IGHJ2 B IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c3 3 1 1 NA NA NA 1 s1c4 S1 IGHV3 IGHJ3 C IGH 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c4 4 4 1 NA NA NA 1 s2c1 S2 IGHV4 IGHJ4 D IGH 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c1 5 6 1 NA NA NA 1 s2c2 S2 IGHV5 IGHJ5 E IGH 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c2 6 5 1 NA NA NA 1 s2c3 S2 IGHV5 IGHJ5 E IGH 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c3 7 5 1 NA NA NA 1 s2c4 S2 IGHV6 IGHJ6 F IGH 5 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c4 8 2 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 4 NA 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:230:3 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-downsample.R:230:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n=1 receptor mode agg schema: sample_id input annotation shape: 8x13 input repertoire shape: annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, 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 s1c1 S1 IGHV1 IGHJ1 A IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c1 1 3 1 0 s1c2 S1 IGHV1 IGHJ1 A IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c2 2 3 1 0 s1c3 S1 IGHV2 IGHJ2 B IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c3 3 1 1 0 s1c4 S1 IGHV3 IGHJ3 C IGH 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c4 4 4 1 0 s2c1 S2 IGHV4 IGHJ4 D IGH 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c1 5 6 1 0 s2c2 S2 IGHV5 IGHJ5 E IGH 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c2 6 5 1 0 s2c3 S2 IGHV5 IGHJ5 E IGH 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c3 7 5 1 0 s2c4 S2 IGHV6 IGHJ6 F IGH 5 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c4 8 2 1 0 input repertoires dump: 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 s1c1 S1 IGHV1 IGHJ1 A IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c1 1 3 1 NA NA NA 1 s1c2 S1 IGHV1 IGHJ1 A IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c2 2 3 1 NA NA NA 1 s1c3 S1 IGHV2 IGHJ2 B IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c3 3 1 1 NA NA NA 1 s1c4 S1 IGHV3 IGHJ3 C IGH 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c4 4 4 1 NA NA NA 1 s2c1 S2 IGHV4 IGHJ4 D IGH 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c1 5 6 1 NA NA NA 1 s2c2 S2 IGHV5 IGHJ5 E IGH 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c2 6 5 1 NA NA NA 1 s2c3 S2 IGHV5 IGHJ5 E IGH 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c3 7 5 1 NA NA NA 1 s2c4 S2 IGHV6 IGHJ6 F IGH 5 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c4 8 2 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 4 NA 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:230:3 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-downsample.R:230:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample n=1 receptor mode agg schema: sample_id input annotation shape: 8x13 input repertoire shape: annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, 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 s1c1 S1 IGHV1 IGHJ1 A IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c1 1 3 1 0 s1c2 S1 IGHV1 IGHJ1 A IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c2 2 3 1 0 s1c3 S1 IGHV2 IGHJ2 B IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c3 3 1 1 0 s1c4 S1 IGHV3 IGHJ3 C IGH 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c4 4 4 1 0 s2c1 S2 IGHV4 IGHJ4 D IGH 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c1 5 6 1 0 s2c2 S2 IGHV5 IGHJ5 E IGH 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c2 6 5 1 0 s2c3 S2 IGHV5 IGHJ5 E IGH 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c3 7 5 1 0 s2c4 S2 IGHV6 IGHJ6 F IGH 5 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c4 8 2 1 0 input repertoires dump: 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 s1c1 S1 IGHV1 IGHJ1 A IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c1 1 3 1 NA NA NA 1 s1c2 S1 IGHV1 IGHJ1 A IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c2 2 3 1 NA NA NA 1 s1c3 S1 IGHV2 IGHJ2 B IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c3 3 1 1 NA NA NA 1 s1c4 S1 IGHV3 IGHJ3 C IGH 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s1c4 4 4 1 NA NA NA 1 s2c1 S2 IGHV4 IGHJ4 D IGH 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c1 5 6 1 NA NA NA 1 s2c2 S2 IGHV5 IGHJ5 E IGH 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c2 6 5 1 NA NA NA 1 s2c3 S2 IGHV5 IGHJ5 E IGH 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c3 7 5 1 NA NA NA 1 s2c4 S2 IGHV6 IGHJ6 F IGH 5 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a067b04f85.tsv s2c4 8 2 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 4 NA 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:230:3 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 ── Error ('test-downsample.R:236:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Error in `select(sampled_receptors, all_of(receptor_join_cols))`: i In argument: `all_of(receptor_join_cols)`. Caused by error in `all_of()`: ! Can't subset elements that don't exist. x Elements `imd_repertoire_id` and `imd_receptor_id` don't exist. ── Failure ('test-downsample.R:322:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n exceeds units agg schema: sample_id input annotation shape: 6x13 input repertoire shape: annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, 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 c1 S1 IGHV1 IGHJ1 A1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c1 1 4 1 0 c2 S1 IGHV2 IGHJ2 A2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c2 2 5 1 0 c3 S1 IGHV3 IGHJ3 A3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c3 3 3 1 0 c4 S2 IGHV1 IGHJ1 B1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c4 4 1 1 0 c5 S2 IGHV2 IGHJ2 B2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c5 5 2 1 0 c6 S2 IGHV3 IGHJ3 B3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c6 6 6 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 A1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c1 1 4 1 NA NA NA 1 c2 S1 IGHV2 IGHJ2 A2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c2 2 5 1 NA NA NA 1 c3 S1 IGHV3 IGHJ3 A3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c3 3 3 1 NA NA NA 1 c4 S2 IGHV1 IGHJ1 B1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c4 4 1 1 NA NA NA 1 c5 S2 IGHV2 IGHJ2 B2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c5 5 2 1 NA NA NA 1 c6 S2 IGHV3 IGHJ3 B3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c6 6 6 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 3 NA 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:322:3 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-downsample.R:322:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n exceeds units agg schema: sample_id input annotation shape: 6x13 input repertoire shape: annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, 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 c1 S1 IGHV1 IGHJ1 A1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c1 1 4 1 0 c2 S1 IGHV2 IGHJ2 A2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c2 2 5 1 0 c3 S1 IGHV3 IGHJ3 A3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c3 3 3 1 0 c4 S2 IGHV1 IGHJ1 B1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c4 4 1 1 0 c5 S2 IGHV2 IGHJ2 B2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c5 5 2 1 0 c6 S2 IGHV3 IGHJ3 B3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c6 6 6 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 A1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c1 1 4 1 NA NA NA 1 c2 S1 IGHV2 IGHJ2 A2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c2 2 5 1 NA NA NA 1 c3 S1 IGHV3 IGHJ3 A3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c3 3 3 1 NA NA NA 1 c4 S2 IGHV1 IGHJ1 B1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c4 4 1 1 NA NA NA 1 c5 S2 IGHV2 IGHJ2 B2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c5 5 2 1 NA NA NA 1 c6 S2 IGHV3 IGHJ3 B3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c6 6 6 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 3 NA 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:322:3 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-downsample.R:322:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample n exceeds units agg schema: sample_id input annotation shape: 6x13 input repertoire shape: annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, 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 c1 S1 IGHV1 IGHJ1 A1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c1 1 4 1 0 c2 S1 IGHV2 IGHJ2 A2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c2 2 5 1 0 c3 S1 IGHV3 IGHJ3 A3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c3 3 3 1 0 c4 S2 IGHV1 IGHJ1 B1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c4 4 1 1 0 c5 S2 IGHV2 IGHJ2 B2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c5 5 2 1 0 c6 S2 IGHV3 IGHJ3 B3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c6 6 6 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 A1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c1 1 4 1 NA NA NA 1 c2 S1 IGHV2 IGHJ2 A2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c2 2 5 1 NA NA NA 1 c3 S1 IGHV3 IGHJ3 A3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c3 3 3 1 NA NA NA 1 c4 S2 IGHV1 IGHJ1 B1 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c4 4 1 1 NA NA NA 1 c5 S2 IGHV2 IGHJ2 B2 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c5 5 2 1 NA NA NA 1 c6 S2 IGHV3 IGHJ3 B3 IGH 1 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a016ce200d.tsv c6 6 6 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 3 NA 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:322:3 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 ── Error ('test-downsample.R:333:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Error in `downsample_immundata(idata, n = 10, seed = 42)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-downsample.R:333:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─immundata::downsample_immundata(idata, n = 10, seed = 42) 8. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 9. └─rlang::abort(...) ── Failure ('test-downsample.R:370:3'): downsample_immundata supports count-mode proportion downsampling ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count proportion agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:370:3 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-downsample.R:370:3'): downsample_immundata supports count-mode proportion downsampling ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count proportion agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:370:3 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-downsample.R:370:3'): downsample_immundata supports count-mode proportion downsampling ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample count proportion agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04a16560.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:370:3 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 ── Error ('test-downsample.R:376:3'): downsample_immundata supports count-mode proportion downsampling ── Error in `downsample_immundata(idata, n = 0.5, seed = 101)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 0.5, seed = 101) at test-downsample.R:376:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:407:3'): downsample_immundata is deterministic in count mode with seed ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count deterministic agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:407:3 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-downsample.R:407:3'): downsample_immundata is deterministic in count mode with seed ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count deterministic agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:407:3 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-downsample.R:407:3'): downsample_immundata is deterministic in count mode with seed ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample count deterministic agg schema: sample_id input annotation shape: 4x11 input repertoire shape: annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA input annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 1 1 1 8 0 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 2 2 3 7 0 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 3 3 4 6 0 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 4 4 2 9 0 input repertoires dump: annotations dump: sample_id v_call j_call junction_aa clone_count filename imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires S1 TRBV1 TRBJ1 AAAA 8 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 1 1 1 8 NA NA NA 1 S1 TRBV2 TRBJ2 BBBB 7 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 2 2 3 7 NA NA NA 1 S2 TRBV3 TRBJ1 CCCC 6 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 3 3 4 6 NA NA NA 1 S2 TRBV4 TRBJ2 DDDD 9 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a03c2a671a.tsv 4 4 2 9 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 15 NA 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:407:3 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 ── Error ('test-downsample.R:413:3'): downsample_immundata is deterministic in count mode with seed ── Error in `downsample_immundata(idata, n = 5, seed = 222)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 5, seed = 222) at test-downsample.R:413:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:466:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count/proportion invariants agg schema: sample_id input annotation shape: 6x13 input repertoire shape: annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, 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 c1 S1 IGHV1 IGHJ1 A1 IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c1 1 3 1 0 c2 S1 IGHV1 IGHJ1 A1 IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c2 2 3 1 0 c3 S1 IGHV2 IGHJ2 A2 IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c3 3 4 1 0 c4 S2 IGHV1 IGHJ1 B1 IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c4 4 1 1 0 c5 S2 IGHV2 IGHJ2 B2 IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c5 5 2 1 0 c6 S2 IGHV2 IGHJ2 B2 IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c6 6 2 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 A1 IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c1 1 3 1 NA NA NA 1 c2 S1 IGHV1 IGHJ1 A1 IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c2 2 3 1 NA NA NA 1 c3 S1 IGHV2 IGHJ2 A2 IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c3 3 4 1 NA NA NA 1 c4 S2 IGHV1 IGHJ1 B1 IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c4 4 1 1 NA NA NA 1 c5 S2 IGHV2 IGHJ2 B2 IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c5 5 2 1 NA NA NA 1 c6 S2 IGHV2 IGHJ2 B2 IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c6 6 2 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 3 NA 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:466:3 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-downsample.R:466:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count/proportion invariants agg schema: sample_id input annotation shape: 6x13 input repertoire shape: annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, 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 c1 S1 IGHV1 IGHJ1 A1 IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c1 1 3 1 0 c2 S1 IGHV1 IGHJ1 A1 IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c2 2 3 1 0 c3 S1 IGHV2 IGHJ2 A2 IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c3 3 4 1 0 c4 S2 IGHV1 IGHJ1 B1 IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c4 4 1 1 0 c5 S2 IGHV2 IGHJ2 B2 IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c5 5 2 1 0 c6 S2 IGHV2 IGHJ2 B2 IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c6 6 2 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 A1 IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c1 1 3 1 NA NA NA 1 c2 S1 IGHV1 IGHJ1 A1 IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c2 2 3 1 NA NA NA 1 c3 S1 IGHV2 IGHJ2 A2 IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c3 3 4 1 NA NA NA 1 c4 S2 IGHV1 IGHJ1 B1 IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c4 4 1 1 NA NA NA 1 c5 S2 IGHV2 IGHJ2 B2 IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c5 5 2 1 NA NA NA 1 c6 S2 IGHV2 IGHJ2 B2 IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c6 6 2 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 3 NA 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:466:3 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-downsample.R:466:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample count/proportion invariants agg schema: sample_id input annotation shape: 6x13 input repertoire shape: annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, 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 c1 S1 IGHV1 IGHJ1 A1 IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c1 1 3 1 0 c2 S1 IGHV1 IGHJ1 A1 IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c2 2 3 1 0 c3 S1 IGHV2 IGHJ2 A2 IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c3 3 4 1 0 c4 S2 IGHV1 IGHJ1 B1 IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c4 4 1 1 0 c5 S2 IGHV2 IGHJ2 B2 IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c5 5 2 1 0 c6 S2 IGHV2 IGHJ2 B2 IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c6 6 2 1 0 input repertoires dump: 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 c1 S1 IGHV1 IGHJ1 A1 IGH 10 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c1 1 3 1 NA NA NA 1 c2 S1 IGHV1 IGHJ1 A1 IGH 11 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c2 2 3 1 NA NA NA 1 c3 S1 IGHV2 IGHJ2 A2 IGH 12 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c3 3 4 1 NA NA NA 1 c4 S2 IGHV1 IGHJ1 B1 IGH 13 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c4 4 1 1 NA NA NA 1 c5 S2 IGHV2 IGHJ2 B2 IGH 14 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c5 5 2 1 NA NA NA 1 c6 S2 IGHV2 IGHJ2 B2 IGH 15 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpgffA4V\\file8a04462ee3.tsv c6 6 2 1 NA NA NA 1 repertoires dump: imd_repertoire_id sample_id n_barcodes n_receptors 1 S1 3 NA 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::agg_repertoires_with_integrity(...) at test-downsample.R:466:3 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 ── Error ('test-downsample.R:472:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Error in `downsample_immundata(idata, n = 2, seed = 33)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 2, seed = 33) at test-downsample.R:472:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── 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: annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: 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_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell5 5 1 1 0 input repertoires dump: 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_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.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: annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: 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_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell5 5 1 1 0 input repertoires dump: 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_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.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: annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: 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_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell1 1 3 1 0 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell2 2 3 1 0 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell3 3 4 1 0 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell4 4 2 1 0 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell5 5 1 1 0 input repertoires dump: 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_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell1 1 3 1 NA NA NA 1 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell2 2 3 1 NA NA NA 1 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell3 3 4 1 NA NA NA 1 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.tsv cell4 4 2 1 NA NA NA 1 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 D:\\temp\\2026_03_15_23_35_17_2377\\RtmpaI1emF\\filea5104e2c4e26.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 35 | WARN 0 | SKIP 0 | PASS 358 ] Error: ! Test failures. Execution halted