* using log directory 'd:/RCompile/CRANincoming/R-devel/immundata.Rcheck' * using R Under development (unstable) (2026-03-14 r89623 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-03-15 22:15:29 UTC * checking for file 'immundata/DESCRIPTION' ... OK * this is package 'immundata' version '0.0.6' * package encoding: UTF-8 * checking CRAN incoming feasibility ... OK * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'immundata' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [182s] ERROR Running 'testthat.R' [182s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 8. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c44d04903/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c44d04903/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c44d04903] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c44d04903'] > test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c44d04903'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 2.93 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6d1c1f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6d1c1f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6d1c1f] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6d1c1f'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6d1c1f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.8 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc174d52f/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc174d52f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc174d52f] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc174d52f'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc174d52f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.67 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c54d6512/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c54d6512/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c54d6512] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c54d6512'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c54d6512'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.14 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5de926a5/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5de926a5/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5de926a5] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5de926a5'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5de926a5'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.91 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5bb409e/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5bb409e/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5bb409e] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5bb409e'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5bb409e'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.06 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 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: > 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 Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1cc8189b/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1cc8189b/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1cc8189b] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1cc8189b'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1cc8189b'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.98 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc51b73972/annotations.parquet] > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc51b73972/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc51b73972] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc51b73972'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc51b73972'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.95 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c7faf5fe3/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c7faf5fe3/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c7faf5fe3] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c7faf5fe3'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c7faf5fe3'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.07 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3407328/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3407328/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3407328] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3407328'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3407328'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.93 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c4e6139a4/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c4e6139a4/metadata.json] > test-annotate-external.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c4e6139a4] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c4e6139a4'] > test-annotate-external.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c4e6139a4'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 2.98 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6a8a499a/annotations.parquet] > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6a8a499a/metadata.json] > test-annotate-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c326e4d/annotations.parquet] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6a8a499a] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6a8a499a'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6a8a499a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.86 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c326e4d/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c326e4d] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c326e4d'] > test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c326e4d'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 3.06 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427ca5a741e/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427ca5a741e/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427ca5a741e] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427ca5a741e'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427ca5a741e'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.89 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-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: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc16774fad/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc16774fad/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc16774fad] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc16774fad'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc16774fad'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.89 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c39763f7c/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c39763f7c/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c39763f7c] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c39763f7c'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c39763f7c'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.97 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: 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-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c11964396/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6656425e/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c11964396/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c11964396] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c11964396'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c11964396'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.91 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6656425e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6656425e] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6656425e'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6656425e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: i Time elapsed: 3.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-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: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c353684b/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c353684b/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c353684b] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c353684b'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c353684b'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 3.82 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c40226569.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc4f2734d/annotations.parquet] > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c558f4222/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c558f4222/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c558f4222] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c558f4222'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c558f4222'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.32 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [8] chains and [8] receptors > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc4f2734d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc4f2734d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc4f2734d'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc4f2734d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.96 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c328949dd.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-agg-strata.R: 1. exclude_columns > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c1af53b2d/annotations.parquet] > test-agg-strata.R: 2. filter_nonproductive > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c1af53b2d/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c1af53b2d] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c1af53b2d'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c1af53b2d'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.15 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL] > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3ff71973.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c599232f/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c599232f/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c599232f] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c599232f'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c599232f'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 2.02 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-downsample.R: v Loaded ImmunData with [12] chains and [6] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae3f7a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae3f7a/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae3f7a] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae3f7a'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae3f7a'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.01 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. > test-downsample.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-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-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-agg-strata.R: 2. filter_nonproductive > test-downsample.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2e0119cb/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2e0119cb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2e0119cb] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2e0119cb'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2e0119cb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.83 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc15de30ab/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc15de30ab/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc15de30ab] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc15de30ab'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc15de30ab'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.75 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc7f68759d/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc7f68759d/metadata.json] > test-agg-strata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc7f68759d] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc7f68759d'] > test-agg-strata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc7f68759d'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.79 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca79144d/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca79144d/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca79144d] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca79144d'] > test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca79144d'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 3 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c156d4371/annotations.parquet] > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-immundata-exact.R: 1. prefix_barcodes > test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-exact.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc22436e7b/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc22436e7b/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc22436e7b] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc22436e7b'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc22436e7b'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 2.97 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c156d4371/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c156d4371] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c156d4371'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c156d4371'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 20.9 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-downsample.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca63d12/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca63d12/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca63d12] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca63d12'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca63d12'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.13 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427ce516b84.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c617c7abc/annotations.parquet] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c617c7abc/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c617c7abc] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c617c7abc'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c617c7abc'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.35 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [8] chains and [6] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-downsample.R: 2. > test-downsample.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: > test-downsample.R: -- Renaming the columns and schemas > test-downsample.R: v Renaming is finished > test-downsample.R: > test-downsample.R: -- Preprocessing the data > test-downsample.R: 1. exclude_columns > test-downsample.R: 2. filter_nonproductive > test-downsample.R: v Preprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc703b3397/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc703b3397/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc703b3397] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc703b3397'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc703b3397'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.03 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Postprocessing the data > test-downsample.R: 1. prefix_barcodes > test-downsample.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-downsample.R: v Postprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c696e47f6/annotations.parquet] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c696e47f6/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c696e47f6] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c696e47f6'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c696e47f6'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 3.01 secs > test-filter-immundata-lev.R: 2. filter_nonproductive > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-downsample.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3f4d32b8.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c16f22d92/annotations.parquet] > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c16f22d92/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c16f22d92] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c16f22d92'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c16f22d92'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.33 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [6] chains and [6] receptors > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c12bcb19.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2017397d/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2017397d/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2017397d] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2017397d'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2017397d'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.15 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL] > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae325e2/annotations.parquet] > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c41d32ec8.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c7a13ef/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c7a13ef/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c7a13ef] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c7a13ef'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c7a13ef'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.15 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and NULL] > test-downsample.R: v Loaded ImmunData with [4] chains and [4] receptors > test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae325e2/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae325e2] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae325e2'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bcae325e2'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.18 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-downsample.R: 2. > test-downsample.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-downsample.R: > test-downsample.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-downsample.R: v Renaming is finished > test-downsample.R: > test-downsample.R: -- Preprocessing the data > test-downsample.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-downsample.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: v Preprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i No locus information found > test-downsample.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Postprocessing the data > test-downsample.R: 1. prefix_barcodes > test-downsample.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-downsample.R: v Postprocessing plan is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-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-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c47df186b/annotations.parquet] > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc266e4ebb/annotations.parquet] > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c47df186b/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c47df186b] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c47df186b'] > test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc266e4ebb/metadata.json] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c47df186b'] > test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc266e4ebb] > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc266e4ebb'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 2.95 secs > test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc266e4ebb'] > test-filter-immundata-regex.R: > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 3.05 secs > test-downsample.R: v Loaded ImmunData with [1902] chains and [1668] receptors > 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-downsample.R: > test-downsample.R: -- Reading repertoire data > test-downsample.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1fea6278.tsv > test-downsample.R: i Checking if all files are of the same type > test-downsample.R: v All files have the same extension > test-downsample.R: > test-downsample.R: -- Aggregating the data to receptors > test-downsample.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-downsample.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-filter-immundata.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-downsample.R: v Execution plan for receptor data aggregation and annotation is ready > test-downsample.R: > test-downsample.R: -- Saving the newly created ImmunData to disk > test-downsample.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c75f57d2d/annotations.parquet] > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-downsample.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c75f57d2d/metadata.json] > test-downsample.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c75f57d2d] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c75f57d2d'] > test-downsample.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c75f57d2d'] > test-downsample.R: > test-downsample.R: -- Summary > test-downsample.R: i Time elapsed: 0.38 secs > test-downsample.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-downsample.R: v Loaded ImmunData with [6] chains and [4] receptors > test-filter-immundata.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 Saving _problems/test-downsample-34.R Saving _problems/test-downsample-34.R Saving _problems/test-downsample-34.R Saving _problems/test-downsample-36.R Saving _problems/test-downsample-83.R Saving _problems/test-downsample-83.R Saving _problems/test-downsample-83.R Saving _problems/test-downsample-85.R Saving _problems/test-downsample-219.R Saving _problems/test-downsample-219.R Saving _problems/test-downsample-219.R Saving _problems/test-downsample-221.R Saving _problems/test-downsample-308.R Saving _problems/test-downsample-308.R Saving _problems/test-downsample-308.R Saving _problems/test-downsample-318.R Saving _problems/test-downsample-353.R Saving _problems/test-downsample-353.R Saving _problems/test-downsample-353.R Saving _problems/test-downsample-355.R Saving _problems/test-downsample-387.R Saving _problems/test-downsample-387.R Saving _problems/test-downsample-387.R Saving _problems/test-downsample-389.R Saving _problems/test-downsample-443.R Saving _problems/test-downsample-443.R Saving _problems/test-downsample-443.R Saving _problems/test-downsample-445.R > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc240855ea/annotations.parquet] > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3a18384b/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc240855ea/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc240855ea] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc240855ea'] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc240855ea'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.93 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-receptors.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3a18384b/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3a18384b] > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3a18384b'] > test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c3a18384b'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 2.96 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\legacy_v1_427c63c47b04/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\legacy_v1_427c63c47b04/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\legacy_v1_427c63c47b04] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\legacy_v1_427c63c47b04'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\legacy_v1_427c63c47b04'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.34 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\legacy_v1_427c63c47b04'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2938275c/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-filter-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2938275c/metadata.json] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2938275c] > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2938275c'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc2938275c'] > test-io-immundata.R: i Time elapsed: 1.33 secs > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.09 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc58bb118b.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc401319a3/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc401319a3/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc401319a3] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc401319a3'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc401319a3'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.37 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.45 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > 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: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc38805bac.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > 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 All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc7aa11ff8/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.39 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\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_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc7aa11ff8/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc7aa11ff8] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc7aa11ff8'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc7aa11ff8'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.65 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc38e53f2a.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc8103e20/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc8103e20/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc8103e20] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc8103e20'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc8103e20'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 2.28 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.31 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 [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc1caa5622.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bca58208/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.4 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\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-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bca58208/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bca58208] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bca58208'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bca58208'] > 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: > test-io-repertoires-agg.R: -- Summary > 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 Time elapsed: 1.54 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc795384c.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.42 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\treated\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\treated\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\treated\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\treated\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB'] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6ec24bae/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6ec24bae/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6ec24bae] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6ec24bae'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6ec24bae'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.58 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bca253c21.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.42 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v002'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3e7a504b/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3e7a504b/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3e7a504b] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3e7a504b'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3e7a504b'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.51 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 [2] chains and [1] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] Saving _problems/test-io-repertoires-agg-44.R Saving _problems/test-io-repertoires-agg-44.R Saving _problems/test-io-repertoires-agg-44.R Saving _problems/test-io-repertoires-agg-61.R Saving _problems/test-io-repertoires-agg-67.R Saving _problems/test-io-repertoires-agg-85.R Saving _problems/test-io-repertoires-agg-93.R > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc20572f69.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.4 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-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 Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc634e2e06/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc634e2e06/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc634e2e06] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc634e2e06'] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc634e2e06'] > 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 [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3bcc630f.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-immundata.R: v Renaming is finished > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > 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: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc44db29b3/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc44db29b3/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc44db29b3] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc44db29b3'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc44db29b3'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.32 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc16251f3b.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc70357a73/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc70357a73/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc70357a73] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc70357a73'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc70357a73'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.56 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc793a1924.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c69755e5f/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c69755e5f/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c69755e5f] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c69755e5f'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c69755e5f'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.11 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > 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: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc59c228fd/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-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc59c228fd/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc59c228fd] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc59c228fd'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc59c228fd'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.38 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc104b6a89.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.35 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001/metadata.json] > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc484c42b5/annotations.parquet] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\baseline\v001'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB\snapshots\baseline\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB\snapshots\baseline\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectB\snapshots\baseline\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\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: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc484c42b5/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc484c42b5] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc484c42b5'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc484c42b5'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.58 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc6e6a38eb.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.39 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\ops\v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\ops\v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\imd_snap_tests\projectA\snapshots\ops\v001] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\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-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3c205287/annotations.parquet] > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3c205287/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3c205287] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3c205287'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3c205287'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.48 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3b585a98.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc65fa2ef9/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc65fa2ef9/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc65fa2ef9] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc65fa2ef9'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc65fa2ef9'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.17 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5535075.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1971c18/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc37ac1703/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1971c18/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1971c18] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1971c18'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c1971c18'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.92 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-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc37ac1703/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc37ac1703] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc37ac1703'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc37ac1703'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 2.19 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc5535075.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc35b3bae/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5a9f5b8d/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc35b3bae/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc35b3bae] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc35b3bae'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc35b3bae'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.96 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_03_15_23_15_17_31227\RtmpyMeWkc\file427c5a9f5b8d/metadata.json] > test-io-immundata.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5a9f5b8d] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5a9f5b8d'] > test-io-immundata.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c5a9f5b8d'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.01 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcc604ecb/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcc604ecb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcc604ecb] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcc604ecb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcc604ecb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.32 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.41 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.71 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc356235df/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc356235df/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc356235df] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc356235df'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc356235df'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.5 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.4 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc48d56555/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:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc48d56555/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc48d56555] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc48d56555'] > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc48d56555'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.45 secs > test-io-repertoires-processing.R: i Time elapsed: 1.65 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: 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:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\immundata-sample_0_1k'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.3 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-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: 1000 Columns: 40 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal... > test-io-repertoires-processing.R: dbl (5): clone_id, v_score, d_score, j_score, counts > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_... > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc24e675be/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc24e675be/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc24e675be] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc24e675be'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc24e675be'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.12 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc5249539a/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc5249539a/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc5249539a] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc5249539a'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc5249539a'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.12 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc245b70e9/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc245b70e9/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc245b70e9] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc245b70e9'] > test-io-repertoires-files.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc245b70e9'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.08 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c6c895450/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c6c895450/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c6c895450] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c6c895450'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c6c895450'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 20.05 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\ig\multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c312d2d3c/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c312d2d3c/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c312d2d3c] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c312d2d3c'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c312d2d3c'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 3.51 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c18ff4696.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c79833f55/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c79833f55/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c79833f55] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c79833f55'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c79833f55'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.32 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\file427c52fe1836.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-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3b9467ab/annotations.parquet] > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2f853ed2/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2f853ed2/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2f853ed2] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2f853ed2'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test_immundata_427c2f853ed2'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.33 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpyMeWkc\test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 1.68 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-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3b9467ab/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3b9467ab] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3b9467ab'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc3b9467ab'] > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema-paired.R: i Time elapsed: 20.45 secs > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema-paired.R: > 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.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. D:\RCompile\CRANincoming\R-devel\lib\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6d637c05/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6d637c05/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6d637c05] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6d637c05'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc6d637c05'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 20.95 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc3843125b.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcf674223/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcf674223/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcf674223] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcf674223'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bcf674223'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.38 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\file80bc23661a7d.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc1e786464/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc1e786464/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc1e786464] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc1e786464'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['D:\temp\2026_03_15_23_15_17_31227\RtmpkNOecj\test_immundata_80bc1e786464'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.29 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 35 | WARN 0 | SKIP 0 | PASS 358 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-downsample.R:34:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample single-cell deterministic annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 8 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 CARA IGH 10 "D:\\temp\\2026_0~ 2 c2 S1 IGHV2 IGHJ2 CARB IGH 11 "D:\\temp\\2026_0~ 3 c3 S1 IGHV3 IGHJ3 CARC IGH 12 "D:\\temp\\2026_0~ 4 c4 S1 IGHV4 IGHJ4 CARD IGH 13 "D:\\temp\\2026_0~ 5 c5 S2 IGHV1 IGHJ1 CARE IGH 14 "D:\\temp\\2026_0~ 6 c6 S2 IGHV2 IGHJ2 CARF IGH 15 "D:\\temp\\2026_0~ 7 c7 S2 IGHV3 IGHJ3 CARG IGH 16 "D:\\temp\\2026_0~ 8 c8 S2 IGHV4 IGHJ4 CARH IGH 17 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 4 NA 2 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample single-cell deterministic") at test-downsample.R:34:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:34:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample single-cell deterministic annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 8 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 CARA IGH 10 "D:\\temp\\2026_0~ 2 c2 S1 IGHV2 IGHJ2 CARB IGH 11 "D:\\temp\\2026_0~ 3 c3 S1 IGHV3 IGHJ3 CARC IGH 12 "D:\\temp\\2026_0~ 4 c4 S1 IGHV4 IGHJ4 CARD IGH 13 "D:\\temp\\2026_0~ 5 c5 S2 IGHV1 IGHJ1 CARE IGH 14 "D:\\temp\\2026_0~ 6 c6 S2 IGHV2 IGHJ2 CARF IGH 15 "D:\\temp\\2026_0~ 7 c7 S2 IGHV3 IGHJ3 CARG IGH 16 "D:\\temp\\2026_0~ 8 c8 S2 IGHV4 IGHJ4 CARH IGH 17 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 4 NA 2 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample single-cell deterministic") at test-downsample.R:34:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:34:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample single-cell deterministic annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 8 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 CARA IGH 10 "D:\\temp\\2026_0~ 2 c2 S1 IGHV2 IGHJ2 CARB IGH 11 "D:\\temp\\2026_0~ 3 c3 S1 IGHV3 IGHJ3 CARC IGH 12 "D:\\temp\\2026_0~ 4 c4 S1 IGHV4 IGHJ4 CARD IGH 13 "D:\\temp\\2026_0~ 5 c5 S2 IGHV1 IGHJ1 CARE IGH 14 "D:\\temp\\2026_0~ 6 c6 S2 IGHV2 IGHJ2 CARF IGH 15 "D:\\temp\\2026_0~ 7 c7 S2 IGHV3 IGHJ3 CARG IGH 16 "D:\\temp\\2026_0~ 8 c8 S2 IGHV4 IGHJ4 CARH IGH 17 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 4 NA 2 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample single-cell deterministic") at test-downsample.R:34:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:36:3'): downsample_immundata downsamples single-cell repertoires and is deterministic with seed ── Error in `downsample_immundata(idata, n = 2, seed = 100)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 2, seed = 100) at test-downsample.R:36:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:83:3'): downsample_immundata downsampled bulk repertoires by count ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample bulk count mode annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample bulk count mode") at test-downsample.R:83:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:83:3'): downsample_immundata downsampled bulk repertoires by count ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample bulk count mode annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample bulk count mode") at test-downsample.R:83:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:83:3'): downsample_immundata downsampled bulk repertoires by count ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample bulk count mode annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample bulk count mode") at test-downsample.R:83:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:85:3'): downsample_immundata downsampled bulk repertoires by count ── Error in `downsample_immundata(idata, n = 5, seed = 42)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 5, seed = 42) at test-downsample.R:85:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:219:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n=1 receptor mode annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 8 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 s1c1 S1 IGHV1 IGHJ1 A IGH 12 "D:\\temp\\2026_0~ 2 s1c2 S1 IGHV1 IGHJ1 A IGH 11 "D:\\temp\\2026_0~ 3 s1c3 S1 IGHV2 IGHJ2 B IGH 10 "D:\\temp\\2026_0~ 4 s1c4 S1 IGHV3 IGHJ3 C IGH 9 "D:\\temp\\2026_0~ 5 s2c1 S2 IGHV4 IGHJ4 D IGH 8 "D:\\temp\\2026_0~ 6 s2c2 S2 IGHV5 IGHJ5 E IGH 7 "D:\\temp\\2026_0~ 7 s2c3 S2 IGHV5 IGHJ5 E IGH 6 "D:\\temp\\2026_0~ 8 s2c4 S2 IGHV6 IGHJ6 F IGH 5 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 4 NA 2 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample n=1 receptor mode") at test-downsample.R:219:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:219:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n=1 receptor mode annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 8 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 s1c1 S1 IGHV1 IGHJ1 A IGH 12 "D:\\temp\\2026_0~ 2 s1c2 S1 IGHV1 IGHJ1 A IGH 11 "D:\\temp\\2026_0~ 3 s1c3 S1 IGHV2 IGHJ2 B IGH 10 "D:\\temp\\2026_0~ 4 s1c4 S1 IGHV3 IGHJ3 C IGH 9 "D:\\temp\\2026_0~ 5 s2c1 S2 IGHV4 IGHJ4 D IGH 8 "D:\\temp\\2026_0~ 6 s2c2 S2 IGHV5 IGHJ5 E IGH 7 "D:\\temp\\2026_0~ 7 s2c3 S2 IGHV5 IGHJ5 E IGH 6 "D:\\temp\\2026_0~ 8 s2c4 S2 IGHV6 IGHJ6 F IGH 5 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 4 NA 2 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample n=1 receptor mode") at test-downsample.R:219:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:219:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample n=1 receptor mode annotation shape: 8x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=8, imd_count=8, imd_proportion=8, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 8 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 s1c1 S1 IGHV1 IGHJ1 A IGH 12 "D:\\temp\\2026_0~ 2 s1c2 S1 IGHV1 IGHJ1 A IGH 11 "D:\\temp\\2026_0~ 3 s1c3 S1 IGHV2 IGHJ2 B IGH 10 "D:\\temp\\2026_0~ 4 s1c4 S1 IGHV3 IGHJ3 C IGH 9 "D:\\temp\\2026_0~ 5 s2c1 S2 IGHV4 IGHJ4 D IGH 8 "D:\\temp\\2026_0~ 6 s2c2 S2 IGHV5 IGHJ5 E IGH 7 "D:\\temp\\2026_0~ 7 s2c3 S2 IGHV5 IGHJ5 E IGH 6 "D:\\temp\\2026_0~ 8 s2c4 S2 IGHV6 IGHJ6 F IGH 5 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 4 NA 2 2 S2 4 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample n=1 receptor mode") at test-downsample.R:219:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:221:3'): downsample_immundata with n = 1 keeps one receptor per repertoire ── Error in `select(sampled_receptors, all_of(receptor_join_cols))`: i In argument: `all_of(receptor_join_cols)`. Caused by error in `all_of()`: ! Can't subset elements that don't exist. x Elements `imd_repertoire_id` and `imd_receptor_id` don't exist. ── Failure ('test-downsample.R:308:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n exceeds units annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 6 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 A1 IGH 1 "D:\\temp\\2026_0~ 2 c2 S1 IGHV2 IGHJ2 A2 IGH 1 "D:\\temp\\2026_0~ 3 c3 S1 IGHV3 IGHJ3 A3 IGH 1 "D:\\temp\\2026_0~ 4 c4 S2 IGHV1 IGHJ1 B1 IGH 1 "D:\\temp\\2026_0~ 5 c5 S2 IGHV2 IGHJ2 B2 IGH 1 "D:\\temp\\2026_0~ 6 c6 S2 IGHV3 IGHJ3 B3 IGH 1 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 3 NA 2 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample n exceeds units") at test-downsample.R:308:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:308:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample n exceeds units annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 6 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 A1 IGH 1 "D:\\temp\\2026_0~ 2 c2 S1 IGHV2 IGHJ2 A2 IGH 1 "D:\\temp\\2026_0~ 3 c3 S1 IGHV3 IGHJ3 A3 IGH 1 "D:\\temp\\2026_0~ 4 c4 S2 IGHV1 IGHJ1 B1 IGH 1 "D:\\temp\\2026_0~ 5 c5 S2 IGHV2 IGHJ2 B2 IGH 1 "D:\\temp\\2026_0~ 6 c6 S2 IGHV3 IGHJ3 B3 IGH 1 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 3 NA 2 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample n exceeds units") at test-downsample.R:308:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:308:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample n exceeds units annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 6 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 A1 IGH 1 "D:\\temp\\2026_0~ 2 c2 S1 IGHV2 IGHJ2 A2 IGH 1 "D:\\temp\\2026_0~ 3 c3 S1 IGHV3 IGHJ3 A3 IGH 1 "D:\\temp\\2026_0~ 4 c4 S2 IGHV1 IGHJ1 B1 IGH 1 "D:\\temp\\2026_0~ 5 c5 S2 IGHV2 IGHJ2 B2 IGH 1 "D:\\temp\\2026_0~ 6 c6 S2 IGHV3 IGHJ3 B3 IGH 1 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 3 NA 2 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample n exceeds units") at test-downsample.R:308:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:315:3'): downsample_immundata warns and keeps repertoire unchanged when n exceeds available units ── Error in `downsample_immundata(idata, n = 10, seed = 42)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-downsample.R:315:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─immundata::downsample_immundata(idata, n = 10, seed = 42) 8. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 9. └─rlang::abort(...) ── Failure ('test-downsample.R:353:3'): downsample_immundata supports count-mode proportion downsampling ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count proportion annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count proportion") at test-downsample.R:353:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:353:3'): downsample_immundata supports count-mode proportion downsampling ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count proportion annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count proportion") at test-downsample.R:353:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:353:3'): downsample_immundata supports count-mode proportion downsampling ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample count proportion annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count proportion") at test-downsample.R:353:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:355:3'): downsample_immundata supports count-mode proportion downsampling ── Error in `downsample_immundata(idata, n = 0.5, seed = 101)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 0.5, seed = 101) at test-downsample.R:355:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:387:3'): downsample_immundata is deterministic in count mode with seed ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count deterministic annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count deterministic") at test-downsample.R:387:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:387:3'): downsample_immundata is deterministic in count mode with seed ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count deterministic annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count deterministic") at test-downsample.R:387:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:387:3'): downsample_immundata is deterministic in count mode with seed ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample count deterministic annotation shape: 4x14 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=4, imd_count=4, imd_proportion=4, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 4 x 14 sample_id v_call j_call junction_aa clone_count filename imd_barcode * 1 S1 TRBV1 TRBJ1 AAAA 8 "D:\\temp\\2026_0~ 1 2 S1 TRBV2 TRBJ2 BBBB 7 "D:\\temp\\2026_0~ 2 3 S2 TRBV3 TRBJ1 CCCC 6 "D:\\temp\\2026_0~ 3 4 S2 TRBV4 TRBJ2 DDDD 9 "D:\\temp\\2026_0~ 4 # i 7 more variables: imd_chain_id , imd_receptor_id , # imd_n_chains , imd_count , imd_repertoire_id , # imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 15 NA 2 2 S2 15 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count deterministic") at test-downsample.R:387:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:389:3'): downsample_immundata is deterministic in count mode with seed ── Error in `downsample_immundata(idata, n = 5, seed = 222)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 5, seed = 222) at test-downsample.R:389:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-downsample.R:443:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count/proportion invariants annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 6 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 A1 IGH 10 "D:\\temp\\2026_0~ 2 c2 S1 IGHV1 IGHJ1 A1 IGH 11 "D:\\temp\\2026_0~ 3 c3 S1 IGHV2 IGHJ2 A2 IGH 12 "D:\\temp\\2026_0~ 4 c4 S2 IGHV1 IGHJ1 B1 IGH 13 "D:\\temp\\2026_0~ 5 c5 S2 IGHV2 IGHJ2 B2 IGH 14 "D:\\temp\\2026_0~ 6 c6 S2 IGHV2 IGHJ2 B2 IGH 15 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 3 NA 2 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count/proportion invariants") at test-downsample.R:443:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-downsample.R:443:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: downsample count/proportion invariants annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 6 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 A1 IGH 10 "D:\\temp\\2026_0~ 2 c2 S1 IGHV1 IGHJ1 A1 IGH 11 "D:\\temp\\2026_0~ 3 c3 S1 IGHV2 IGHJ2 A2 IGH 12 "D:\\temp\\2026_0~ 4 c4 S2 IGHV1 IGHJ1 B1 IGH 13 "D:\\temp\\2026_0~ 5 c5 S2 IGHV2 IGHJ2 B2 IGH 14 "D:\\temp\\2026_0~ 6 c6 S2 IGHV2 IGHJ2 B2 IGH 15 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 3 NA 2 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count/proportion invariants") at test-downsample.R:443:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-downsample.R:443:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: downsample count/proportion invariants annotation shape: 6x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=6, imd_count=6, imd_proportion=6, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 6 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 c1 S1 IGHV1 IGHJ1 A1 IGH 10 "D:\\temp\\2026_0~ 2 c2 S1 IGHV1 IGHJ1 A1 IGH 11 "D:\\temp\\2026_0~ 3 c3 S1 IGHV2 IGHJ2 A2 IGH 12 "D:\\temp\\2026_0~ 4 c4 S2 IGHV1 IGHJ1 B1 IGH 13 "D:\\temp\\2026_0~ 5 c5 S2 IGHV2 IGHJ2 B2 IGH 14 "D:\\temp\\2026_0~ 6 c6 S2 IGHV2 IGHJ2 B2 IGH 15 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 S1 3 NA 2 2 S2 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata, "downsample count/proportion invariants") at test-downsample.R:443:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Error ('test-downsample.R:445:3'): downsample_immundata produces consistent imd_count and imd_proportion invariants ── Error in `downsample_immundata(idata, n = 2, seed = 33)`: No barcode units were selected. Increase `n`. Backtrace: ▆ 1. └─immundata::downsample_immundata(idata, n = 2, seed = 33) at test-downsample.R:445:3 2. └─cli::cli_abort("No barcode units were selected. Increase `n`.") 3. └─rlang::abort(...) ── Failure ('test-io-repertoires-agg.R:44:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(ann_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 5 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 "D:\\temp\\2026_0~ 2 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 "D:\\temp\\2026_0~ 3 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 "D:\\temp\\2026_0~ 4 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 "D:\\temp\\2026_0~ 5 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 Sample2 2 NA 2 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata_agg, "single-chain duplicated receptors") at test-io-repertoires-agg.R:44:3 2. └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:159:5 ── Failure ('test-io-repertoires-agg.R:44:3'): agg_repertoires counts single-chain receptors correctly ── Expected `all(reps_na_counts == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE context: single-chain duplicated receptors annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 5 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 "D:\\temp\\2026_0~ 2 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 "D:\\temp\\2026_0~ 3 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 "D:\\temp\\2026_0~ 4 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 "D:\\temp\\2026_0~ 5 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 Sample2 2 NA 2 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata_agg, "single-chain duplicated receptors") at test-io-repertoires-agg.R:44:3 2. └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:162:5 ── Failure ('test-io-repertoires-agg.R:44:3'): agg_repertoires counts single-chain receptors correctly ── Expected `nrow(unmatched_repertoire_ids)` to equal 0. Differences: `actual`: 1.0 `expected`: 0.0 context: single-chain duplicated receptors annotation shape: 5x16 repertoire shape: 2x4 missing annotation columns: missing repertoire columns: annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0 repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2 unmatched repertoire ids: NA annotations dump: # A tibble: 5 x 16 cell_id sample_id v_call j_call junction_aa locus umi_count filename * 1 cell1 Sample1 IGHV1 IGHJ1 CARW IGH 100 "D:\\temp\\2026_0~ 2 cell2 Sample1 IGHV1 IGHJ1 CARW IGH 150 "D:\\temp\\2026_0~ 3 cell3 Sample1 IGHV2 IGHJ2 CBRW IGH 200 "D:\\temp\\2026_0~ 4 cell4 Sample2 IGHV3 IGHJ3 CCRW IGH 250 "D:\\temp\\2026_0~ 5 cell5 Sample2 IGHV4 IGHJ4 CDRW IGH 300 "D:\\temp\\2026_0~ # i 8 more variables: imd_barcode , imd_chain_id , # imd_receptor_id , imd_n_chains , imd_count , # imd_repertoire_id , imd_proportion , n_repertoires repertoires dump: # A tibble: 2 x 4 imd_repertoire_id sample_id n_barcodes n_receptors 1 1 Sample2 2 NA 2 2 Sample1 3 NA Backtrace: ▆ 1. └─immundata:::expect_agg_repertoires_integrity(idata_agg, "single-chain duplicated receptors") at test-io-repertoires-agg.R:44:3 2. └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:166:5 ── Failure ('test-io-repertoires-agg.R:59:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample1 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:65:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample2_stats$n_receptors` to equal 2. Differences: `actual`: NA `expected`: 2.0 Sample2 should have 2 unique receptors ── Failure ('test-io-repertoires-agg.R:83:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count1[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 ── Failure ('test-io-repertoires-agg.R:91:3'): agg_repertoires counts single-chain receptors correctly ── Expected `sample1_counts$total_count2[1]` to equal 2. Differences: `actual`: NA `expected`: 2.0 Shared receptor should have count of 2 [ FAIL 35 | WARN 0 | SKIP 0 | PASS 358 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR