R version 4.6.0 alpha (2026-04-02 r89777 ucrt) 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: 4. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.7 > > 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-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > 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: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: > 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-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_04_03_14_50_16_5647\Rtmpk787D7\file1885c5b8936b7/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_04_03_14_50_16_5647\Rtmpk787D7\file1885c5b8936b7/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c5b8936b7] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c5b8936b7'] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c5b8936b7'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 5.04 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a358430d102b/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358430d102b/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358430d102b] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358430d102b'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358430d102b'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.54 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35853a96d68/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35853a96d68/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35853a96d68] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35853a96d68'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35853a96d68'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.6 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c60f3399b/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_04_03_14_50_16_5647\Rtmpk787D7\file1885c60f3399b/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c60f3399b] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c60f3399b'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c60f3399b'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.79 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a3586da8160d/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6a002ea2/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3586da8160d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3586da8160d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3586da8160d'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3586da8160d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.51 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c6a002ea2/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6a002ea2] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6a002ea2'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6a002ea2'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.09 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-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > 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-annotate-external.R: 1. exclude_columns > 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: 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c16516e76/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_04_03_14_50_16_5647\Rtmpk787D7\file1885c16516e76/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c16516e76] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c16516e76'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c16516e76'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.01 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35847f3fe6/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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35847f3fe6/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35847f3fe6] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35847f3fe6'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35847f3fe6'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.46 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c6b766142/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6b766142/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6b766142] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6b766142'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6b766142'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.93 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35852b12935/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35852b12935/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35852b12935] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35852b12935'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35852b12935'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.59 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-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_04_03_14_50_16_5647\Rtmpk787D7\file1885c54a43d39/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c54a43d39/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c54a43d39] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c54a43d39'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c54a43d39'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.07 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-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-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_04_03_14_50_16_5647\Rtmpk787D7\file1885c726f4308/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3588b37f7e/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c726f4308/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c726f4308] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c726f4308'] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c726f4308'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3588b37f7e/metadata.json] > test-annotate-receptors.R: i Time elapsed: 5.08 secs > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3588b37f7e] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3588b37f7e'] > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3588b37f7e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.6 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\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_04_03_14_50_16_5647\Rtmpk787D7\file1885c68c954c7/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_04_03_14_50_16_5647\Rtmpk787D7\file1885c68c954c7/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c68c954c7] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c68c954c7'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c68c954c7'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.45 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35817c357f5/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35817c357f5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35817c357f5] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35817c357f5'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35817c357f5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.21 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-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: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c6311813/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-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6311813/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6311813] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6311813'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6311813'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.38 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35829a52e05/annotations.parquet] > 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: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35829a52e05/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35829a52e05] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35829a52e05'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35829a52e05'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.48 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-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the 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-compute-collect-immundata.R: 1. prefix_barcodes > 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-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-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c43ba7fa2/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c43ba7fa2/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c43ba7fa2] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c43ba7fa2'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c43ba7fa2'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 5.99 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-agg-strata.R: v 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: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3582c854399/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3582c854399/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3582c854399] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3582c854399'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3582c854399'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.45 secs > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c64fc33db/annotations.parquet] > 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-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c64fc33db/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c64fc33db] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c64fc33db'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c64fc33db'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.18 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-filter-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-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-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_04_03_14_50_16_5647\Rtmpk787D7\file1885c1e534431/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35821dd2431/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c1e534431/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c1e534431] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c1e534431'] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c1e534431'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 5.19 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-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35821dd2431/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35821dd2431] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35821dd2431'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35821dd2431'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.36 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: v 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c197771d3/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c197771d3/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c197771d3] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c197771d3'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c197771d3'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 4.92 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-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-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-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-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_04_03_14_50_16_5647\RtmpAZPqGq\file1a3587f7b616c/annotations.parquet] > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3587f7b616c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3587f7b616c] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3587f7b616c'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3587f7b616c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Time elapsed: 6.27 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-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_04_03_14_50_16_5647\Rtmpk787D7\file1885c3b387fd1/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c3b387fd1/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c3b387fd1] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c3b387fd1'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c3b387fd1'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.96 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35818682805/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35818682805/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35818682805] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35818682805'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35818682805'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.42 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c618c63e4/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c618c63e4/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c618c63e4] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c618c63e4'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c618c63e4'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 5.32 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35876ee15ef/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35876ee15ef/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35876ee15ef] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35876ee15ef'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35876ee15ef'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.18 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-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_04_03_14_50_16_5647\Rtmpk787D7\file1885c142b4272/annotations.parquet] > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c142b4272/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c142b4272] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c142b4272'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c142b4272'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 5.6 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: 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 > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358779576/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358779576/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358779576] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358779576'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358779576'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.97 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. D:\RCompile\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 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: 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 Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c594a5edb/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c594a5edb/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c594a5edb] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c594a5edb'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c594a5edb'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.41 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35816e16145/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35816e16145/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35816e16145] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35816e16145'] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35816e16145'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 5.12 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-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: 1. prefix_barcodes > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\legacy_v1_1a35841607500/annotations.parquet] > 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c30441094/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\legacy_v1_1a35841607500/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\legacy_v1_1a35841607500] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\legacy_v1_1a35841607500'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\legacy_v1_1a35841607500'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.22 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_04_03_14_50_16_5647\RtmpAZPqGq\legacy_v1_1a35841607500'] > 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: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c30441094/metadata.json] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c30441094] > 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 Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c30441094'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c30441094'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 5.25 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c6eb843af.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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3e5587c/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3e5587c/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3e5587c] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3e5587c'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3e5587c'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.59 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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c6cea72aa.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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.25 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [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: 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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c688a7770/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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c688a7770/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c688a7770] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c688a7770'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c688a7770'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.39 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.17 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c67125fd0.tsv > test-io-immundata.R: i No locus information found > test-io-repertoires-agg.R: i Checking if all files are of the same type > 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 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_04_03_14_50_16_5647\RtmpAZPqGq\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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c2cc39e6/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c2cc39e6/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c2cc39e6] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c2cc39e6'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c2cc39e6'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.5 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 [6] chains and [2] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c542a330f.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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885cf5b2257/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885cf5b2257/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885cf5b2257] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885cf5b2257'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885cf5b2257'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.24 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: 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: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c55d96085.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 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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.87 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [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-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c117448aa/annotations.parquet] > 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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c117448aa/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c117448aa] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c117448aa'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c117448aa'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.51 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c54c9687f.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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.23 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\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: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c97e992/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c97e992/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c97e992] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c97e992'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c97e992'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.4 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c22b06f33.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-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1bc3e3a/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1bc3e3a/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1bc3e3a] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1bc3e3a'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1bc3e3a'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.52 secs > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.2 secs > test-io-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-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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c541453b7.tsv > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\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-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > 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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\treated\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\treated\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\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-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c67c6fda/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c67c6fda/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c67c6fda] > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c67c6fda'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c67c6fda'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.58 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c12895b33.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c75c7df0/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.22 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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\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_04_03_14_50_16_5647\RtmpAZPqGq\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-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c75c7df0/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c75c7df0] > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c75c7df0'] > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c75c7df0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.33 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c1639654c.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c26522c62/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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.21 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c26522c62/metadata.json] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c26522c62] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c26522c62'] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c26522c62'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.2 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c24331034.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: 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-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-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c52cc328d/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c52cc328d/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c52cc328d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c52cc328d'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c52cc328d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.31 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c4848247f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1a4f2eda/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_04_03_14_50_16_5647\RtmpAZPqGq\file1a35834b6322/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1a4f2eda/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1a4f2eda] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1a4f2eda'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1a4f2eda'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.65 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c16f53db2.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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c203920be/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c203920be/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c203920be] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c203920be'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c203920be'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.35 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35834b6322/metadata.json] > test-io-repertoires-counts.R: 1. D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\file1885c22fc21.tsv > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35834b6322] > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35834b6322'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a35834b6322'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.55 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- 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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c23b627a7/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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c23b627a7/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c23b627a7] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c23b627a7'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c23b627a7'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.41 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c22fc21.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.3 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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB/annotations.parquet] > 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: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectB\snapshots\baseline\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c7982f2a/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_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c7982f2a/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c7982f2a] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c7982f2a'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c7982f2a'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.54 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > 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-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.26 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\ops\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\imd_snap_tests\projectA\snapshots\ops\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c65d71303/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c65d71303/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c65d71303] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c65d71303'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c65d71303'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.31 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a3583eaccad/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3583eaccad/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3583eaccad] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3583eaccad'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a3583eaccad'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.92 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c79ad6ea/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c79ad6ea/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c79ad6ea] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c79ad6ea'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c79ad6ea'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.16 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-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: > 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a358408e189e/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c519a1342/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358408e189e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358408e189e] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358408e189e'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\file1a358408e189e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.31 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 [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-files.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c519a1342/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c519a1342] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c519a1342'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c519a1342'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.23 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: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > 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-files.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: 1. exclude_columns > 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-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: > 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_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.41 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3dd718cb/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_04_03_14_50_16_5647\RtmpAZPqGq\test-rename/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3dd718cb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3dd718cb] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3dd718cb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c3dd718cb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.11 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-rename] > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-rename'] > 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-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Time elapsed: 3.09 secs > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: v 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-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: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: 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 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_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.39 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-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c6b1a3e02/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_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35840ab6ca2/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c6b1a3e02/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c6b1a3e02] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c6b1a3e02'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c6b1a3e02'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.14 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35840ab6ca2/metadata.json] > 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-processing.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35840ab6ca2] > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35840ab6ca2'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35840ab6ca2'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.82 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: > 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: 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-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_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35831274664/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35831274664/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35831274664] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35831274664'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35831274664'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.09 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-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: 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 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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c626f4823/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c626f4823/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c626f4823] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c626f4823'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c626f4823'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.43 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 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-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_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35849d17bcd/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35849d17bcd/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35849d17bcd] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35849d17bcd'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35849d17bcd'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 31.13 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-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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1f1617d8/annotations.parquet] > 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: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1f1617d8/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1f1617d8] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1f1617d8'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c1f1617d8'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 34.14 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-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_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3582a5321f6/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-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-single.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3582a5321f6/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3582a5321f6] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3582a5321f6'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3582a5321f6'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.76 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a358759c751e.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_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3583a9a72fb/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3583a9a72fb/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3583a9a72fb] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3583a9a72fb'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a3583a9a72fb'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.55 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_04_03_14_50_16_5647\RtmpAZPqGq\file1a358367f53dc.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_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35835366b/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35835366b/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35835366b] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35835366b'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test_immundata_1a35835366b'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.54 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\RtmpAZPqGq\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: 3.16 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c14797006/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c14797006/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c14797006] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c14797006'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c14797006'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 34.05 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c14362843.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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c4731345e/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c4731345e/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c4731345e] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c4731345e'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c4731345e'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 2.15 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_04_03_14_50_16_5647\Rtmpk787D7\file1885c44c56093.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_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c62694dfd/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c62694dfd/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c62694dfd] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c62694dfd'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_04_03_14_50_16_5647\Rtmpk787D7\test_immundata_1885c62694dfd'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.98 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 0 | WARN 0 | SKIP 0 | PASS 323 ] > > proc.time() user system elapsed 6.84 1.20 250.81