Running ‘testthat.R’ [187s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > 
  > library(immundata)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: duckplyr
  The duckplyr package is configured to fall back to dplyr when it encounters an
  incompatibility. Fallback events can be collected and uploaded for analysis to
  guide future development. By default, data will be collected but no data will
  be uploaded.
  ℹ Automatic fallback uploading is not controlled and therefore disabled, see
    `?duckplyr::fallback()`.
  ✔ Number of reports ready for upload: 1.
  → Review with `duckplyr::fallback_review()`, upload with
    `duckplyr::fallback_upload()`.
  ℹ Configure automatic uploading with `duckplyr::fallback_config()`.
  ✔ Overwriting dplyr methods with duckplyr methods.
  ℹ Turn off with `duckplyr::methods_restore()`.
  Loading immundata version 0.0.6
  > 
  > test_check("immundata")
  Starting 2 test processes.
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Reading repertoire data 
  > test-annotate-barcodes.R:   1.
  > test-annotate-barcodes.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-barcodes.R:   2.
  > test-annotate-barcodes.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-agg-strata.R: 
  > test-agg-strata.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: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-annotate-barcodes.R:   2. filter_nonproductive
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d/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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d/metadata.json]
  > test-annotate-barcodes.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d']
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7e8b059d']
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Summary 
  > test-annotate-barcodes.R: i Time elapsed: 2.24 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23111f91e57f']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.85 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4/annotations.parquet]
  > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Postprocessing the data 
  > test-annotate-external.R:   1. prefix_barcodes
  > test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-external.R: v Postprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23113cdebaf4']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.84 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74]
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74']
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f7b243a74']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.33 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: 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Reading repertoire data 
  > test-annotate-external.R:   1.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-annotate-external.R: v Renaming is finished
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Preprocessing the data 
  > test-annotate-external.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573]
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573']
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f610cb573']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.17 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.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 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 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 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1/annotations.parquet]
  > test-annotate-external.R: v Preprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Aggregating the data to receptors 
  > test-annotate-external.R: i No locus information found
  > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231159e153c1']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.82 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256]
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256']
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f312eb256']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.16 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.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231120ea53a5']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.83 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc/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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc]
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc']
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6fdbf2cc']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.17 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.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486/annotations.parquet]
  > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Postprocessing the data 
  > test-annotate-external.R:   1. prefix_barcodes
  > test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-external.R: v Postprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-external.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114a525486']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.84 secs
  > test-annotate-external.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61/metadata.json]
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-external.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61]
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61']
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-annotate-external.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f73c44b61']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 2.16 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: 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-receptors.R: 
  > test-annotate-receptors.R: -- Reading repertoire data 
  > test-annotate-receptors.R:   1.
  > test-annotate-receptors.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-receptors.R:   2.
  > test-annotate-receptors.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-receptors.R: i Checking if all files are of the same type
  > test-annotate-receptors.R: v All files have the same extension
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Renaming the columns and schemas 
  > test-agg-strata.R:   2. filter_nonproductive
  > 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-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-annotate-receptors.R: 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-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Postprocessing the data 
  > test-annotate-receptors.R:   1. prefix_barcodes
  > test-annotate-receptors.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-receptors.R: v Postprocessing plan is ready
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-receptors.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c/annotations.parquet]
  > test-annotate-receptors.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c/metadata.json]
  > test-annotate-receptors.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c]
  > test-annotate-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c']
  > test-annotate-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f53c6a23c']
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Summary 
  > test-annotate-receptors.R: i Time elapsed: 2.16 secs
  > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: 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: 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.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105/annotations.parquet]
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23115795105']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.82 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-compute-collect-immundata.R: v 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f5572599f']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 2.83 secs
  > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > 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 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.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: v Preprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-compute-collect-immundata.R: i No locus information found
  > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23114b4dcd97']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.82 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: v 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 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 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f1159d077']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 2.83 secs
  > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-compute-collect-immundata.R: Rows: 2 Columns: 4
  > test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
  > test-compute-collect-immundata.R: Delimiter: "\t"
  > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-compute-collect-immundata.R: v Metadata parsed successfully
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Reading repertoire data 
  > test-compute-collect-immundata.R:   1.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: v Preprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-compute-collect-immundata.R: i No locus information found
  > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117a376702']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.83 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v 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 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 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f6e85b71e']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 2.83 secs
  > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-compute-collect-immundata.R: Rows: 2 Columns: 4
  > test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
  > test-compute-collect-immundata.R: Delimiter: "\t"
  > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-compute-collect-immundata.R: v Metadata parsed successfully
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Reading repertoire data 
  > test-compute-collect-immundata.R:   1.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: v Preprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-compute-collect-immundata.R: i No locus information found
  > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231160d3385c']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.83 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 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: 
  > 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 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f392e3675']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 2.84 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-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Reading repertoire data 
  > test-filter-barcodes.R:   1.
  > test-filter-barcodes.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-barcodes.R:   2.
  > test-filter-barcodes.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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 [/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231115be3455']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.84 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3/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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-filter-barcodes.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3/metadata.json]
  > test-filter-barcodes.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3]
  > test-filter-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3']
  > test-filter-barcodes.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f322c7ee3']
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Summary 
  > test-filter-barcodes.R: i Time elapsed: 2.16 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.
  > test-filter-immundata-exact.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-exact.R:   2.
  > test-filter-immundata-exact.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-exact.R: i Checking if all files are of the same type
  > test-filter-immundata-exact.R: v All files have the same extension
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-exact.R: v 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-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-immundata-exact.R: v 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9/annotations.parquet]
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-filter-immundata-exact.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9/metadata.json]
  > test-filter-immundata-exact.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9']
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f227f1aa9']
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Summary 
  > test-filter-immundata-exact.R: i Time elapsed: 2.17 secs
  > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: v 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3/annotations.parquet]
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Reading repertoire data 
  > test-filter-immundata-hamm.R:   1.
  > test-filter-immundata-hamm.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-hamm.R:   2.
  > test-filter-immundata-hamm.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3/metadata.json]
  > test-filter-immundata-hamm.R:   2. filter_nonproductive
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231125d9d3f3']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.84 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-hamm.R: v Preprocessing plan is ready
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Aggregating the data to receptors 
  > test-filter-immundata-hamm.R: i No locus information found
  > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Postprocessing the data 
  > test-filter-immundata-hamm.R:   1. prefix_barcodes
  > test-filter-immundata-hamm.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-hamm.R: v Postprocessing plan is ready
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c/annotations.parquet]
  > test-filter-immundata-hamm.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c/metadata.json]
  > test-filter-immundata-hamm.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c']
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f3cbab83c']
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Summary 
  > test-filter-immundata-hamm.R: i Time elapsed: 2.16 secs
  > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Reading repertoire data 
  > test-filter-immundata-lev.R:   1.
  > test-filter-immundata-lev.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-lev.R:   2.
  > test-filter-immundata-lev.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-lev.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R: v All files have the same extension
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > test-filter-immundata-lev.R: v Renaming is finished
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Preprocessing the data 
  > test-filter-immundata-lev.R:   1. exclude_columns
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311514b5982']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.83 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.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Postprocessing the data 
  > test-filter-immundata-lev.R:   1. prefix_barcodes
  > test-filter-immundata-lev.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-lev.R: v Postprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4/annotations.parquet]
  > test-filter-immundata-lev.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f54b336a4']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 2.19 secs
  > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Reading repertoire data 
  > test-filter-immundata-lev.R:   1.
  > test-filter-immundata-lev.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-lev.R:   2.
  > test-filter-immundata-lev.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-lev.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R: v All files have the same extension
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > test-filter-immundata-lev.R: v Renaming is finished
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Preprocessing the data 
  > test-filter-immundata-lev.R:   1. exclude_columns
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751]
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751']
  > test-agg-strata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311343b8751']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 2.84 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Reading repertoire data 
  > test-filter-immundata-regex.R:   1.
  > test-filter-immundata-regex.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-regex.R:   2.
  > test-filter-immundata-regex.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-regex.R: i Checking if all files are of the same type
  > test-filter-immundata-regex.R: v All files have the same extension
  > test-filter-immundata-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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675/annotations.parquet]
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Renaming the columns and schemas 
  > test-filter-immundata-regex.R: v Renaming is finished
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Preprocessing the data 
  > test-filter-immundata-regex.R:   1. exclude_columns
  > test-filter-immundata-regex.R:   2. filter_nonproductive
  > test-filter-immundata-lev.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f4cb52675']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 2.16 secs
  > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata.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.
  > test-filter-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata.R:   2.
  > test-filter-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata.R: i Checking if all files are of the same type
  > test-filter-immundata.R: v All files have the same extension
  > test-filter-immundata-regex.R: v Preprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Aggregating the data to receptors 
  > test-filter-immundata-regex.R: i No locus information found
  > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: v Renaming is finished
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Preprocessing the data 
  > test-filter-immundata.R:   1. exclude_columns
  > test-filter-immundata.R:   2. filter_nonproductive
  > test-filter-immundata.R: v Preprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Aggregating the data to receptors 
  > test-filter-immundata.R: i No locus information found
  > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Postprocessing the data 
  > test-filter-immundata-regex.R:   1. prefix_barcodes
  > test-filter-immundata-regex.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-regex.R: v Postprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469/annotations.parquet]
  > test-filter-immundata-regex.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469/metadata.json]
  > test-filter-immundata-regex.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469']
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231164ca8469']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Summary 
  > test-filter-immundata-regex.R: i Time elapsed: 2.2 secs
  > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Reading repertoire data 
  > test-filter-receptors.R:   1.
  > test-filter-receptors.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-receptors.R:   2.
  > test-filter-receptors.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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-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 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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf/annotations.parquet]
  > test-filter-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf]
  > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf']
  > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f58a2fdaf']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 2.81 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.
  > test-filter-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata.R:   2.
  > test-filter-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata.R: i Checking if all files are of the same type
  > test-filter-immundata.R: v All files have the same extension
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: v Renaming is finished
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Preprocessing the data 
  > test-filter-immundata.R:   1. exclude_columns
  > test-filter-immundata.R:   2. filter_nonproductive
  > test-filter-immundata.R: v Preprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Aggregating the data to receptors 
  > test-filter-immundata.R: i No locus information found
  > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Postprocessing the data 
  > test-filter-receptors.R:   1. prefix_barcodes
  > test-filter-receptors.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-receptors.R: v Postprocessing plan is ready
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Saving the newly created ImmunData to disk 
  > test-filter-receptors.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff/annotations.parquet]
  > test-filter-receptors.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff/metadata.json]
  > test-filter-receptors.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff]
  > test-filter-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff']
  > test-filter-receptors.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311378a47ff']
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Summary 
  > test-filter-receptors.R: i Time elapsed: 2.2 secs
  > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4/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 [/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623/annotations.parquet]
  > test-filter-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4]
  > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4']
  > test-filter-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/file230f44d39ad4']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 2.18 secs
  > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-io-repertoires-agg-stepwise.R: 
  > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data 
  > test-io-repertoires-agg-stepwise.R:   1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f7e35cd23.tsv
  > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type
  > test-io-repertoires-agg-stepwise.R: v All files have the same extension
  > test-io-repertoires-agg-stepwise.R: 
  > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors 
  > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-agg-stepwise.R: 
  > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623']
  > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4/metadata.json]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4]
  > test-io-immundata.R: i Time elapsed: 0.97 secs
  > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4']
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3acb60a4']
  > test-io-repertoires-agg-stepwise.R: 
  > test-io-repertoires-agg-stepwise.R: -- Summary 
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.09 secs
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/legacy_v1_231113301623']
  > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  Saving _problems/test-io-repertoires-agg-stepwise-125.R
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f2ecd8018']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.08 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-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f55edf0bd.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963/annotations.parquet]
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f59fe8963']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.32 secs
  > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-repertoires-agg.R:   1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f63140bec.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-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.98 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > 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-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f51d898be']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.3 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3840c472.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f76fba8e']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.26 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f78438bc2.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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.98 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476/annotations.parquet]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f381ef476']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.33 secs
  > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3d5de9c4.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-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3898e2fb']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.32 secs
  > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors
  Saving _problems/test-io-repertoires-agg-47.R
  Saving _problems/test-io-repertoires-agg-47.R
  Saving _problems/test-io-repertoires-agg-47.R
  Saving _problems/test-io-repertoires-agg-64.R
  Saving _problems/test-io-repertoires-agg-70.R
  Saving _problems/test-io-repertoires-agg-88.R
  Saving _problems/test-io-repertoires-agg-96.R
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-repertoires-counts.R:   1. /Volumes/Temp/tmp/RtmpdlzRHI/file230ff2f326c.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f572255cd']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.08 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f66b020bc.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1110cfa4']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.09 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f49c92ba5.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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.99 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2/annotations.parquet]
  > test-io-immundata.R: Rows: 2 Columns: 4
  > test-io-immundata.R: -- Column specification --------------------------------------------------------
  > test-io-immundata.R: Delimiter: "\t"
  > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix
  > test-io-immundata.R: 
  > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-io-immundata.R: v Metadata parsed successfully
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f67449da2']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.3 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and 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-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-repertoires-counts.R:   1. /Volumes/Temp/tmp/RtmpdlzRHI/file230f43dc476f.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 Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f4c680fa9']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.27 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f75e8f74f.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f7a3a0049']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.28 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f25d33203.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f622bbe2f']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.33 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3f94e743.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f40ff664b']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.05 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f33ddb98e.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f74dd51b3']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.27 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f33ddb98e.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: -- Joining the metadata table with the dataset using 'filename' column 
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6e1efab5']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.33 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")]
  > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Reading repertoire data 
  > test-io-repertoires-files.R:   1.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v 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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.41 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f78bb9ffc']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 0.97 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.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.97 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.98 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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/treated/v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f16c5ec7a']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 1.87 secs
  > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > 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.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-immundata.R: v 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-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.99 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v002']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/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 ['/Volumes/Temp/tmp/RtmpZg4BKT/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.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff/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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f440949ff']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 1.87 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.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.99 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > 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-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Preprocessing the data 
  > test-io-immundata.R:   1. exclude_columns
  > test-io-immundata.R:   2. filter_nonproductive
  > test-io-immundata.R: v Preprocessing plan is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column 
  > 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 [/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92/annotations.parquet]
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file23117fa45f92']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.18 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f3aab38e6']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 2.38 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-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-immundata.R: 
  > 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-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.97 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB']
  > test-io-immundata.R: i Writing the receptor annotation data to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectB/snapshots/baseline/v001']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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-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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 0.98 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 [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/imd_snap_tests/projectA/snapshots/ops/v001']
  > 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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce/annotations.parquet]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Preprocessing the data 
  > test-io-immundata.R:   1. exclude_columns
  > test-io-immundata.R:   2. filter_nonproductive
  > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f37f1bdce']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 2.38 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.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-immundata.R: v Preprocessing plan is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: v 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-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 [/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file2311392b96b8']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.2 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3/annotations.parquet]
  > test-io-immundata.R:   2. filter_nonproductive
  > test-io-immundata.R: v Preprocessing plan is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230fe35f8f3']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 2.38 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-processing.R: 
  > test-io-repertoires-processing.R: -- Reading repertoire data 
  > test-io-repertoires-processing.R:   1.
  > test-io-repertoires-processing.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-processing.R: i Checking if all files are of the same type
  > test-io-repertoires-processing.R: v All files have the same extension
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Renaming the columns and schemas 
  > test-io-repertoires-processing.R: v Renaming is finished
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Preprocessing the data 
  > test-io-repertoires-processing.R:   1. exclude_columns
  > test-io-repertoires-processing.R: v Preprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.02 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.
  > test-io-repertoires-processing.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-processing.R: i Checking if all files are of the same type
  > test-io-repertoires-processing.R: v All files have the same extension
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Renaming the columns and schemas 
  > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene
  > test-io-repertoires-processing.R: v Renaming is finished
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Preprocessing the data 
  > test-io-repertoires-processing.R:   1. exclude_columns
  > test-io-repertoires-processing.R:   2. filter_nonproductive
  > test-io-repertoires-processing.R: v Preprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-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 [/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28]
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28']
  > test-io-immundata.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/file231188d6e28']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 2.18 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] 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:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/ig/multiple_ig_loci.tsv.gz
  > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type
  > test-io-repertoires-schema-paired.R: v All files have the same extension
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors 
  > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- 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 [/Volumes/Temp/tmp/RtmpdlzRHI/test-rename/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-rename/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-rename]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-rename']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-rename']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.14 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:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-processing.R: i Checking if all files are of the same type
  > test-io-repertoires-processing.R: v All files have the same extension
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Renaming the columns and schemas 
  > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene
  > test-io-repertoires-processing.R: v Renaming is finished
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Preprocessing the data 
  > test-io-repertoires-processing.R:   1. exclude_columns
  > test-io-repertoires-processing.R: v Preprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-exclude-rename']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.02 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.
  > test-io-repertoires-processing.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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 [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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: 1.2 secs
  > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors
  > test-io-repertoires-processing.R: Rows: 1000 Columns: 40
  > test-io-repertoires-processing.R: -- Column specification --------------------------------------------------------
  > test-io-repertoires-processing.R: Delimiter: "\t"
  > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal...
  > test-io-repertoires-processing.R: dbl  (5): clone_id, v_score, d_score, j_score, counts
  > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_...
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Reading repertoire data 
  > test-io-repertoires-processing.R:   1.
  > test-io-repertoires-processing.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/immundata-sample_0_1k']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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: 0.98 secs
  > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-repertoires-processing.R: Rows: 1000 Columns: 40
  > test-io-repertoires-processing.R: -- Column specification --------------------------------------------------------
  > test-io-repertoires-processing.R: Delimiter: "\t"
  > test-io-repertoires-processing.R: chr (16): sequence_id, repertoire_id, locus, sequence, v_call, d_call, j_cal...
  > test-io-repertoires-processing.R: dbl  (5): clone_id, v_score, d_score, j_score, counts
  > test-io-repertoires-processing.R: lgl (19): stop_codon, vj_in_frame, productive, fwr1, cdr1, fwr2, cdr2, fwr1_...
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-repertoires-processing.R: Rows: 2 Columns: 4
  > test-io-repertoires-processing.R: -- Column specification --------------------------------------------------------
  > test-io-repertoires-processing.R: Delimiter: "\t"
  > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-io-repertoires-processing.R: v Metadata parsed successfully
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Reading repertoire data 
  > test-io-repertoires-processing.R:   1.
  > test-io-repertoires-processing.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-processing.R:   2.
  > test-io-repertoires-processing.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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-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 [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_2311419e21fb']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 12.91 secs
  > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")]
  > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Reading repertoire data 
  > test-io-repertoires-schema-paired.R:   1.
  > test-io-repertoires-schema-paired.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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-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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f57d14d9b']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 15.22 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:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f6259bc67']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 2.16 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f3e871302.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f323ee27b']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 0.08 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. /Volumes/Temp/tmp/RtmpdlzRHI/file230f20ec914b.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 [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test_immundata_230f1c7e31a2']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 0.08 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.
  > test-io-repertoires-schema-table.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes/annotations.parquet]
  > test-io-repertoires-schema-table.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes/metadata.json]
  > test-io-repertoires-schema-table.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes]
  > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/test-no-barcodes']
  > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpdlzRHI/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: 1.15 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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-schema.R: i Checking if all files are of the same type
  > test-io-repertoires-schema.R: v All files have the same extension
  > test-io-repertoires-schema.R: 
  > test-io-repertoires-schema.R: -- Renaming the columns and schemas 
  > test-io-repertoires-schema-paired.R: 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 [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf/annotations.parquet]
  > 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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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.
  > test-io-repertoires-schema.R:   /Volumes/Builds/packages/sonoma-arm64/results/4.6/immundata.Rcheck/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 [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23114504acbf']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 12.93 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. /Volumes/Temp/tmp/RtmpZg4BKT/file2311644c5e21.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 [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_23111beb0bb0']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 0.3 secs
  > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Reading repertoire data 
  > test-io-repertoires-schema-paired.R:   1. /Volumes/Temp/tmp/RtmpZg4BKT/file23115e5458a7.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 [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/Volumes/Temp/tmp/RtmpZg4BKT/test_immundata_231178b98ee4']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 0.33 secs
  > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-io-repertoires-agg-stepwise.R:125:3'): agg_repertoires single-chain stepwise materialized path is stable ──
  <duckdb_error/rlang_error/error/condition>
  Error in `(function (context, message, error_type = NULL, raw_message = NULL, extra_info = NULL)  {     fields <- list()     fields$context <- context     fields$error_type <- error_type     fields$raw_message <- raw_message     fields$extra_info <- extra_info     error_parts <- c(message, i = paste0("Context: ", context))     if (!is.null(error_type)) {         error_parts <- c(error_parts, i = paste0("Error type: ", error_type))     }     if (length(extra_info) > 0) {         info_text <- paste0(names(extra_info), ": ", extra_info)         names(info_text) <- rep_len("i", length(info_text))         error_parts <- c(error_parts, info_text)     }     rlang::abort(error_parts, class = "duckdb_error", !!!fields) })("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n0        duckdb::Exception::Exception(duckdb::ExceptionType, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 52\n1        duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 20\n2        duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&) + 136\n3        duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 616\n4        duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 476\n5        duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&) + 1148\n6        duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&) + 68\n7        duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1972\n8        duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n9        duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n10       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n11       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n12       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n13       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n14       duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long long, true, std::__1::allocator<unsigned long long>>&) + 84\n15       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n16       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n17       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n18       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n19       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n20       duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 136\n21       duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 48\n22       duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters) + 1376\n23       duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode) + 800\n24       duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&) + 128\n25       duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 272\n26       duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 1840\n27       duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool) + 220\n28       duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters) + 588\n29       duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&) + 132\n30       duckdb::Relation::Execute() + 124\n31       duckdb::AltrepRelationWrapper::Materialize() + 292\n32       duckdb::AltrepRelationWrapper::GetQueryResult() + 692\n33       RelToAltrep::RownamesLength(SEXPREC*) + 104\n34       do_shortRowNames + 292\n35       bcEval_loop + 20580\n36       bcEval + 628\n37       Rf_eval + 356\n38       R_execClosure + 796\n39       applyClosure_core + 164\n40       Rf_applyClosure + 12\n41       dispatchMethod + 1236\n42       Rf_usemethod + 520\n43       Rf_DispatchOrEval + 888\n44       do_dim + 112\n45       bcEval_loop + 20580\n46       bcEval + 628\n47       Rf_eval + 356\n48       R_execClosure + 796\n49       applyClosure_core + 164\n50       Rf_applyClosure + 12\n51       dispatchMethod + 1236\n52       Rf_usemethod + 764\n53       do_usemethod + 600\n54       bcEval_loop + 30772\n55       bcEval + 628\n56       Rf_eval + 356\n57       R_execClosure + 796\n58       applyClosure_core + 164\n59       Rf_applyClosure + 12\n60       dispatchMethod + 1236\n61       Rf_usemethod + 764\n62       do_usemethod + 600\n63       bcEval_loop + 30772\n64       bcEval + 628\n65       Rf_eval + 356\n66       R_execClosure + 796\n67       applyClosure_core + 164\n68       Rf_eval + 1640\n69       do_set + 356\n70       Rf_eval + 1024\n71       do_begin + 404\n72       Rf_eval + 1024\n73       do_eval + 1340\n74       bcEval_loop + 20580\n75       bcEval + 628\n76       Rf_eval + 356\n77       R_execClosure + 796\n78       applyClosure_core + 164\n79       Rf_eval + 1640\n80       do_eval + 1928\n81       bcEval_loop + 20580\n82       bcEval + 628\n83       Rf_eval + 356\n84       R_execClosure + 796\n85       applyClosure_core + 164\n86       Rf_eval + 1640\n87       do_begin + 404\n88       Rf_eval + 1024\n89       R_execClosure + 796\n90       applyClosure_core + 164\n91       Rf_eval + 1640\n92       do_docall + 628\n93       bcEval_loop + 20580\n94       bcEval + 628\n95       Rf_eval + 356\n96       R_execClosure + 796\n97       applyClosure_core + 164\n98       Rf_eval + 1640\n99       do_docall + 628\n100      bcEval_loop + 20580\n101      bcEval + 628\n102      Rf_eval + 356\n103      R_execClosure + 796\n104      applyClosure_core + 164\n105      Rf_eval + 1640\n106      forcePromise + 248\n107      getvar + 412\n108      bcEval_loop + 42712\n109      bcEval + 628\n110      Rf_eval + 356\n111      R_execClosure + 796\n112      applyClosure_core + 164\n113      Rf_eval + 1640\n114      do_begin + 404\n115      Rf_eval + 1024\n116      forcePromise + 248\n117      getvar + 412\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")`: Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference "imd_barcode" [42.0]: inequal types (VARCHAR != INTEGER)
  
  Stack Trace:
  
  0        duckdb::Exception::Exception(duckdb::ExceptionType, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 52
  1        duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 20
  2        duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&) + 136
  3        duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 616
  4        duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 476
  5        duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&) + 1148
  6        duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&) + 68
  7        duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1972
  8        duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108
  9        duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960
  10       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108
  11       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960
  12       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108
  13       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960
  14       duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long long, true, std::__1::allocator<unsigned long long>>&) + 84
  15       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960
  16       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108
  17       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960
  18       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108
  19       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960
  20       duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 136
  21       duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 48
  22       duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters) + 1376
  23       duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode) + 800
  24       duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&) + 128
  25       duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 272
  26       duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 1840
  27       duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool) + 220
  28       duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters) + 588
  29       duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&) + 132
  30       duckdb::Relation::Execute() + 124
  31       duckdb::AltrepRelationWrapper::Materialize() + 292
  32       duckdb::AltrepRelationWrapper::GetQueryResult() + 692
  33       RelToAltrep::RownamesLength(SEXPREC*) + 104
  34       do_shortRowNames + 292
  35       bcEval_loop + 20580
  36       bcEval + 628
  37       Rf_eval + 356
  38       R_execClosure + 796
  39       applyClosure_core + 164
  40       Rf_applyClosure + 12
  41       dispatchMethod + 1236
  42       Rf_usemethod + 520
  43       Rf_DispatchOrEval + 888
  44       do_dim + 112
  45       bcEval_loop + 20580
  46       bcEval + 628
  47       Rf_eval + 356
  48       R_execClosure + 796
  49       applyClosure_core + 164
  50       Rf_applyClosure + 12
  51       dispatchMethod + 1236
  52       Rf_usemethod + 764
  53       do_usemethod + 600
  54       bcEval_loop + 30772
  55       bcEval + 628
  56       Rf_eval + 356
  57       R_execClosure + 796
  58       applyClosure_core + 164
  59       Rf_applyClosure + 12
  60       dispatchMethod + 1236
  61       Rf_usemethod + 764
  62       do_usemethod + 600
  63       bcEval_loop + 30772
  64       bcEval + 628
  65       Rf_eval + 356
  66       R_execClosure + 796
  67       applyClosure_core + 164
  68       Rf_eval + 1640
  69       do_set + 356
  70       Rf_eval + 1024
  71       do_begin + 404
  72       Rf_eval + 1024
  73       do_eval + 1340
  74       bcEval_loop + 20580
  75       bcEval + 628
  76       Rf_eval + 356
  77       R_execClosure + 796
  78       applyClosure_core + 164
  79       Rf_eval + 1640
  80       do_eval + 1928
  81       bcEval_loop + 20580
  82       bcEval + 628
  83       Rf_eval + 356
  84       R_execClosure + 796
  85       applyClosure_core + 164
  86       Rf_eval + 1640
  87       do_begin + 404
  88       Rf_eval + 1024
  89       R_execClosure + 796
  90       applyClosure_core + 164
  91       Rf_eval + 1640
  92       do_docall + 628
  93       bcEval_loop + 20580
  94       bcEval + 628
  95       Rf_eval + 356
  96       R_execClosure + 796
  97       applyClosure_core + 164
  98       Rf_eval + 1640
  99       do_docall + 628
  100      bcEval_loop + 20580
  101      bcEval + 628
  102      Rf_eval + 356
  103      R_execClosure + 796
  104      applyClosure_core + 164
  105      Rf_eval + 1640
  106      forcePromise + 248
  107      getvar + 412
  108      bcEval_loop + 42712
  109      bcEval + 628
  110      Rf_eval + 356
  111      R_execClosure + 796
  112      applyClosure_core + 164
  113      Rf_eval + 1640
  114      do_begin + 404
  115      Rf_eval + 1024
  116      forcePromise + 248
  117      getvar + 412
  
  This error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.
  For more information, see https://duckdb.org/docs/stable/dev/internal_errors
  i Context: GetQueryResult
  Backtrace:
       ▆
    1. ├─dplyr::collect(single_chain_annotations) at test-io-repertoires-agg-stepwise.R:125:3
    2. ├─duckplyr:::collect.prudent_duckplyr_df(single_chain_annotations)
    3. │ ├─dplyr::collect(out)
    4. │ └─duckplyr:::collect.duckplyr_df(out)
    5. │   └─base::nrow(x)
    6. │     ├─base::dim(x)
    7. │     └─base::dim.data.frame(x)
    8. │       └─base::.row_names_info(x, 2L)
    9. └─duckdb (local) `<fn>`("GetQueryResult", "Error evaluating duckdb query: INTERNAL Error: Failed to bind column reference \"imd_barcode\" [42.0]: inequal types (VARCHAR != INTEGER)\n\nStack Trace:\n\n0        duckdb::Exception::Exception(duckdb::ExceptionType, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 52\n1        duckdb::InternalException::InternalException(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 20\n2        duckdb::InternalException::InternalException<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, unsigned long long&, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&) + 136\n3        duckdb::ColumnBindingResolver::VisitReplace(duckdb::BoundColumnRefExpression&, duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 616\n4        duckdb::LogicalOperatorVisitor::VisitExpression(duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*) + 476\n5        duckdb::LogicalOperatorVisitor::EnumerateExpressions(duckdb::LogicalOperator&, std::__1::function<void (duckdb::unique_ptr<duckdb::Expression, std::__1::default_delete<duckdb::Expression>, true>*)> const&) + 1148\n6        duckdb::LogicalOperatorVisitor::VisitOperatorExpressions(duckdb::LogicalOperator&) + 68\n7        duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1972\n8        duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n9        duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n10       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n11       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n12       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n13       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n14       duckdb::LogicalOperatorVisitor::VisitChildOfOperatorWithProjectionMap(duckdb::LogicalOperator&, duckdb::vector<unsigned long long, true, std::__1::allocator<unsigned long long>>&) + 84\n15       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n16       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n17       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n18       duckdb::LogicalOperatorVisitor::VisitOperatorChildren(duckdb::LogicalOperator&) + 108\n19       duckdb::ColumnBindingResolver::VisitOperator(duckdb::LogicalOperator&) + 1960\n20       duckdb::PhysicalPlanGenerator::ResolveAndPlan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 136\n21       duckdb::PhysicalPlanGenerator::Plan(duckdb::unique_ptr<duckdb::LogicalOperator, std::__1::default_delete<duckdb::LogicalOperator>, true>) + 48\n22       duckdb::ClientContext::CreatePreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters) + 1376\n23       duckdb::ClientContext::CreatePreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters, duckdb::PreparedStatementMode) + 800\n24       duckdb::ClientContext::PendingStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&) + 128\n25       duckdb::ClientContext::PendingStatementOrPreparedStatement(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 272\n26       duckdb::ClientContext::PendingStatementOrPreparedStatementInternal(duckdb::ClientContextLock&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::shared_ptr<duckdb::PreparedStatementData, true>&, duckdb::PendingQueryParameters const&) + 1840\n27       duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::unique_ptr<duckdb::SQLStatement, std::__1::default_delete<duckdb::SQLStatement>, true>, duckdb::PendingQueryParameters const&, bool) + 220\n28       duckdb::ClientContext::PendingQueryInternal(duckdb::ClientContextLock&, duckdb::shared_ptr<duckdb::Relation, true> const&, duckdb::QueryParameters) + 588\n29       duckdb::ClientContext::Execute(duckdb::shared_ptr<duckdb::Relation, true> const&) + 132\n30       duckdb::Relation::Execute() + 124\n31       duckdb::AltrepRelationWrapper::Materialize() + 292\n32       duckdb::AltrepRelationWrapper::GetQueryResult() + 692\n33       RelToAltrep::RownamesLength(SEXPREC*) + 104\n34       do_shortRowNames + 292\n35       bcEval_loop + 20580\n36       bcEval + 628\n37       Rf_eval + 356\n38       R_execClosure + 796\n39       applyClosure_core + 164\n40       Rf_applyClosure + 12\n41       dispatchMethod + 1236\n42       Rf_usemethod + 520\n43       Rf_DispatchOrEval + 888\n44       do_dim + 112\n45       bcEval_loop + 20580\n46       bcEval + 628\n47       Rf_eval + 356\n48       R_execClosure + 796\n49       applyClosure_core + 164\n50       Rf_applyClosure + 12\n51       dispatchMethod + 1236\n52       Rf_usemethod + 764\n53       do_usemethod + 600\n54       bcEval_loop + 30772\n55       bcEval + 628\n56       Rf_eval + 356\n57       R_execClosure + 796\n58       applyClosure_core + 164\n59       Rf_applyClosure + 12\n60       dispatchMethod + 1236\n61       Rf_usemethod + 764\n62       do_usemethod + 600\n63       bcEval_loop + 30772\n64       bcEval + 628\n65       Rf_eval + 356\n66       R_execClosure + 796\n67       applyClosure_core + 164\n68       Rf_eval + 1640\n69       do_set + 356\n70       Rf_eval + 1024\n71       do_begin + 404\n72       Rf_eval + 1024\n73       do_eval + 1340\n74       bcEval_loop + 20580\n75       bcEval + 628\n76       Rf_eval + 356\n77       R_execClosure + 796\n78       applyClosure_core + 164\n79       Rf_eval + 1640\n80       do_eval + 1928\n81       bcEval_loop + 20580\n82       bcEval + 628\n83       Rf_eval + 356\n84       R_execClosure + 796\n85       applyClosure_core + 164\n86       Rf_eval + 1640\n87       do_begin + 404\n88       Rf_eval + 1024\n89       R_execClosure + 796\n90       applyClosure_core + 164\n91       Rf_eval + 1640\n92       do_docall + 628\n93       bcEval_loop + 20580\n94       bcEval + 628\n95       Rf_eval + 356\n96       R_execClosure + 796\n97       applyClosure_core + 164\n98       Rf_eval + 1640\n99       do_docall + 628\n100      bcEval_loop + 20580\n101      bcEval + 628\n102      Rf_eval + 356\n103      R_execClosure + 796\n104      applyClosure_core + 164\n105      Rf_eval + 1640\n106      forcePromise + 248\n107      getvar + 412\n108      bcEval_loop + 42712\n109      bcEval + 628\n110      Rf_eval + 356\n111      R_execClosure + 796\n112      applyClosure_core + 164\n113      Rf_eval + 1640\n114      do_begin + 404\n115      Rf_eval + 1024\n116      forcePromise + 248\n117      getvar + 412\n\nThis error signals an assertion failure within DuckDB. This usually occurs due to unexpected conditions or errors in the program's logic.\nFor more information, see https://duckdb.org/docs/stable/dev/internal_errors")
   10.   └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
  ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `all(ann_na_counts == 0)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  context: single-chain duplicated receptors
  agg schema: sample_id
  input annotation shape: 5x13
  input repertoire shape: <not captured>
  annotation shape: 5x16
  repertoire shape: 2x4
  missing annotation columns: <none>
  missing repertoire columns: <none>
  annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0
  repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2
  unmatched repertoire ids: NA
  
  input annotations dump:
   cell_id sample_id v_call j_call junction_aa locus umi_count filename                                          imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count
   cell1   Sample1   IGHV1  IGHJ1  CARW        IGH   100       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1       1            3               1            0        
   cell2   Sample1   IGHV1  IGHJ1  CARW        IGH   150       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2       2            3               1            0        
   cell3   Sample1   IGHV2  IGHJ2  CBRW        IGH   200       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3       3            4               1            0        
   cell4   Sample2   IGHV3  IGHJ3  CCRW        IGH   250       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4       4            2               1            0        
   cell5   Sample2   IGHV4  IGHJ4  CDRW        IGH   300       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5       5            1               1            0        
  
  input repertoires dump:
  <NULL>
  
  annotations dump:
   cell_id sample_id v_call j_call junction_aa locus umi_count filename                                          imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires
   cell1   Sample1   IGHV1  IGHJ1  CARW        IGH   100       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1       1            3               1            NA        NA                NA             1            
   cell2   Sample1   IGHV1  IGHJ1  CARW        IGH   150       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2       2            3               1            NA        NA                NA             1            
   cell3   Sample1   IGHV2  IGHJ2  CBRW        IGH   200       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3       3            4               1            NA        NA                NA             1            
   cell4   Sample2   IGHV3  IGHJ3  CCRW        IGH   250       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4       4            2               1            NA        NA                NA             1            
   cell5   Sample2   IGHV4  IGHJ4  CDRW        IGH   300       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5       5            1               1            NA        NA                NA             1            
  
  repertoires dump:
   imd_repertoire_id sample_id n_barcodes n_receptors
   1                 Sample2   2          NA         
   2                 Sample1   3          NA         
  Backtrace:
      ▆
   1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3
   2.   └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3
   3.     └─testthat::expect_true(all(ann_na_counts == 0), info = diag) at ./helper-io.R:205:5
  ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `all(reps_na_counts == 0)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  context: single-chain duplicated receptors
  agg schema: sample_id
  input annotation shape: 5x13
  input repertoire shape: <not captured>
  annotation shape: 5x16
  repertoire shape: 2x4
  missing annotation columns: <none>
  missing repertoire columns: <none>
  annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0
  repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2
  unmatched repertoire ids: NA
  
  input annotations dump:
   cell_id sample_id v_call j_call junction_aa locus umi_count filename                                          imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count
   cell1   Sample1   IGHV1  IGHJ1  CARW        IGH   100       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1       1            3               1            0        
   cell2   Sample1   IGHV1  IGHJ1  CARW        IGH   150       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2       2            3               1            0        
   cell3   Sample1   IGHV2  IGHJ2  CBRW        IGH   200       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3       3            4               1            0        
   cell4   Sample2   IGHV3  IGHJ3  CCRW        IGH   250       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4       4            2               1            0        
   cell5   Sample2   IGHV4  IGHJ4  CDRW        IGH   300       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5       5            1               1            0        
  
  input repertoires dump:
  <NULL>
  
  annotations dump:
   cell_id sample_id v_call j_call junction_aa locus umi_count filename                                          imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires
   cell1   Sample1   IGHV1  IGHJ1  CARW        IGH   100       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1       1            3               1            NA        NA                NA             1            
   cell2   Sample1   IGHV1  IGHJ1  CARW        IGH   150       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2       2            3               1            NA        NA                NA             1            
   cell3   Sample1   IGHV2  IGHJ2  CBRW        IGH   200       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3       3            4               1            NA        NA                NA             1            
   cell4   Sample2   IGHV3  IGHJ3  CCRW        IGH   250       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4       4            2               1            NA        NA                NA             1            
   cell5   Sample2   IGHV4  IGHJ4  CDRW        IGH   300       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5       5            1               1            NA        NA                NA             1            
  
  repertoires dump:
   imd_repertoire_id sample_id n_barcodes n_receptors
   1                 Sample2   2          NA         
   2                 Sample1   3          NA         
  Backtrace:
      ▆
   1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3
   2.   └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3
   3.     └─testthat::expect_true(all(reps_na_counts == 0), info = diag) at ./helper-io.R:208:5
  ── Failure ('test-io-repertoires-agg.R:43:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `nrow(unmatched_repertoire_ids)` to equal 0.
  Differences:
    `actual`: 1.0
  `expected`: 0.0
  
  context: single-chain duplicated receptors
  agg schema: sample_id
  input annotation shape: 5x13
  input repertoire shape: <not captured>
  annotation shape: 5x16
  repertoire shape: 2x4
  missing annotation columns: <none>
  missing repertoire columns: <none>
  annotation NA counts: imd_receptor_id=0, imd_repertoire_id=5, imd_count=5, imd_proportion=5, n_repertoires=0
  repertoire NA counts: imd_repertoire_id=0, n_barcodes=0, n_receptors=2
  unmatched repertoire ids: NA
  
  input annotations dump:
   cell_id sample_id v_call j_call junction_aa locus umi_count filename                                          imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count
   cell1   Sample1   IGHV1  IGHJ1  CARW        IGH   100       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1       1            3               1            0        
   cell2   Sample1   IGHV1  IGHJ1  CARW        IGH   150       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2       2            3               1            0        
   cell3   Sample1   IGHV2  IGHJ2  CBRW        IGH   200       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3       3            4               1            0        
   cell4   Sample2   IGHV3  IGHJ3  CCRW        IGH   250       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4       4            2               1            0        
   cell5   Sample2   IGHV4  IGHJ4  CDRW        IGH   300       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5       5            1               1            0        
  
  input repertoires dump:
  <NULL>
  
  annotations dump:
   cell_id sample_id v_call j_call junction_aa locus umi_count filename                                          imd_barcode imd_chain_id imd_receptor_id imd_n_chains imd_count imd_repertoire_id imd_proportion n_repertoires
   cell1   Sample1   IGHV1  IGHJ1  CARW        IGH   100       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell1       1            3               1            NA        NA                NA             1            
   cell2   Sample1   IGHV1  IGHJ1  CARW        IGH   150       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell2       2            3               1            NA        NA                NA             1            
   cell3   Sample1   IGHV2  IGHJ2  CBRW        IGH   200       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell3       3            4               1            NA        NA                NA             1            
   cell4   Sample2   IGHV3  IGHJ3  CCRW        IGH   250       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell4       4            2               1            NA        NA                NA             1            
   cell5   Sample2   IGHV4  IGHJ4  CDRW        IGH   300       /Volumes/Temp/tmp/RtmpdlzRHI/file230f3594bfa9.tsv cell5       5            1               1            NA        NA                NA             1            
  
  repertoires dump:
   imd_repertoire_id sample_id n_barcodes n_receptors
   1                 Sample2   2          NA         
   2                 Sample1   3          NA         
  Backtrace:
      ▆
   1. └─immundata:::agg_repertoires_with_integrity(...) at test-io-repertoires-agg.R:43:3
   2.   └─immundata:::expect_agg_repertoires_integrity(...) at ./helper-io.R:239:3
   3.     └─testthat::expect_equal(nrow(unmatched_repertoire_ids), 0, info = diag) at ./helper-io.R:212:5
  ── Failure ('test-io-repertoires-agg.R:62:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample1_stats$n_receptors` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Sample1 should have 2 unique receptors
  ── Failure ('test-io-repertoires-agg.R:68:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample2_stats$n_receptors` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Sample2 should have 2 unique receptors
  ── Failure ('test-io-repertoires-agg.R:86:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample1_counts$total_count1[1]` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Shared receptor should have count of 2
  ── Failure ('test-io-repertoires-agg.R:94:3'): agg_repertoires counts single-chain receptors correctly ──
  Expected `sample1_counts$total_count2[1]` to equal 2.
  Differences:
    `actual`:  NA
  `expected`: 2.0
  
  Shared receptor should have count of 2
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 316 ]
  Error:
  ! Test failures.
  Execution halted