Running ‘testthat.R’ [313s/163s]
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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-barcodes.R:   2.
  > test-annotate-barcodes.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Renaming the columns and schemas 
  > test-annotate-barcodes.R: v Renaming is finished
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Preprocessing the data 
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > 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-annotate-barcodes.R:   2. filter_nonproductive
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-annotate-barcodes.R: v Preprocessing plan is ready
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Aggregating the data to receptors 
  > test-annotate-barcodes.R: i No locus information found
  > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Postprocessing the data 
  > test-annotate-barcodes.R:   1. prefix_barcodes
  > test-annotate-barcodes.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-barcodes.R: v Postprocessing plan is ready
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/file24f4296a3af1e6/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 [/tmp/Rtmpr0WkVU/file24f4296a3af1e6/metadata.json]
  > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4296a3af1e6]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4296a3af1e6']
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4296a3af1e6']
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Summary 
  > test-annotate-barcodes.R: i Time elapsed: 3.52 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 [/tmp/Rtmpk8pKcU/file24f3f914f2146d/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f914f2146d/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f914f2146d]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f914f2146d']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f914f2146d']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.42 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-external.R: i Checking if all files are of the same type
  > test-annotate-external.R: v All files have the same extension
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Renaming the columns and schemas 
  > test-annotate-external.R: v Renaming is finished
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Preprocessing the data 
  > test-annotate-external.R:   1. exclude_columns
  > test-annotate-external.R:   2. filter_nonproductive
  > test-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 [/tmp/Rtmpk8pKcU/file24f3f967ef9d7d/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f967ef9d7d/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f967ef9d7d]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f967ef9d7d']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f967ef9d7d']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.1 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpr0WkVU/file24f4291a5a356e/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4291a5a356e/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4291a5a356e]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4291a5a356e']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4291a5a356e']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.83 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpk8pKcU/file24f3f9b6eeb5b/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f9b6eeb5b/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f9b6eeb5b]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9b6eeb5b']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9b6eeb5b']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.05 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Postprocessing the data 
  > test-annotate-external.R:   1. prefix_barcodes
  > test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-external.R: v Postprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/file24f42968b65de3/annotations.parquet]
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f42968b65de3/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f42968b65de3]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42968b65de3']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42968b65de3']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.12 secs
  > 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 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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 [/tmp/Rtmpr0WkVU/file24f42950c9c9ac/annotations.parquet]
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f93616dd07/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f42950c9c9ac/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f42950c9c9ac]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42950c9c9ac']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42950c9c9ac']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.14 secs
  > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f93616dd07/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f93616dd07]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f93616dd07']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f93616dd07']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.02 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Reading repertoire data 
  > test-annotate-external.R:   1.
  > test-annotate-external.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-external.R: i Checking if all files are of the same type
  > test-annotate-external.R: v All files have the same extension
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > 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: 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-annotate-external.R: v 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 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 [/tmp/Rtmpr0WkVU/file24f4296445671/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4296445671/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4296445671]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4296445671']
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4296445671']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-annotate-external.R: i Time elapsed: 3.18 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-external.R:   2.
  > test-annotate-external.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-external.R: i Checking if all files are of the same type
  > test-annotate-external.R: v All files have the same extension
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Renaming the columns and schemas 
  > test-annotate-external.R: v Renaming is finished
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Preprocessing the data 
  > test-annotate-external.R:   1. exclude_columns
  > test-annotate-external.R:   2. filter_nonproductive
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-annotate-external.R: v Preprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Aggregating the data to receptors 
  > test-annotate-external.R: i No locus information found
  > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f94d35ff00/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f94d35ff00/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f94d35ff00]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f94d35ff00']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f94d35ff00']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.13 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpr0WkVU/file24f42939b23e15/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f42939b23e15/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f42939b23e15]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42939b23e15']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42939b23e15']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.21 secs
  > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Reading repertoire data 
  > test-annotate-receptors.R:   1.
  > test-annotate-receptors.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-receptors.R:   2.
  > test-annotate-receptors.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-receptors.R: i Checking if all files are of the same type
  > test-annotate-receptors.R: v All files have the same extension
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Renaming the columns and schemas 
  > test-annotate-receptors.R: v Renaming is finished
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Preprocessing the data 
  > test-annotate-receptors.R:   1. exclude_columns
  > test-annotate-receptors.R:   2. filter_nonproductive
  > test-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 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 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 [/tmp/Rtmpk8pKcU/file24f3f922a0f020/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f922a0f020/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f922a0f020]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f922a0f020']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f922a0f020']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.01 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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 [/tmp/Rtmpr0WkVU/file24f4297ff71fac/annotations.parquet]
  > test-annotate-receptors.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4297ff71fac/metadata.json]
  > test-annotate-receptors.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4297ff71fac]
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4297ff71fac']
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4297ff71fac']
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Summary 
  > test-annotate-receptors.R: i Time elapsed: 3.24 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: 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-agg-strata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-agg-strata.R: v 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 Preprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-compute-collect-immundata.R: i No locus information found
  > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f94eb66fd4/annotations.parquet]
  > test-compute-collect-immundata.R: v Joining plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Postprocessing the data 
  > test-compute-collect-immundata.R:   1. prefix_barcodes
  > test-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 [/tmp/Rtmpr0WkVU/file24f4297d35f69a/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f94eb66fd4/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f94eb66fd4]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f94eb66fd4']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f94eb66fd4']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.15 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: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4297d35f69a/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4297d35f69a]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4297d35f69a']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4297d35f69a']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.18 secs
  > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: v Preprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-compute-collect-immundata.R: i No locus information found
  > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpr0WkVU/file24f4293740602d/annotations.parquet]
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4293740602d/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4293740602d]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4293740602d']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4293740602d']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.46 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-compute-collect-immundata.R: i Checking if all files are of the same type
  > test-compute-collect-immundata.R: v All files have the same extension
  > test-agg-strata.R: v Joining plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-agg-strata.R: v 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 [/tmp/Rtmpk8pKcU/file24f3f97961b79c/annotations.parquet]
  > 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: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f97961b79c/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f97961b79c]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f97961b79c']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f97961b79c']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.99 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpr0WkVU/file24f429978f563/annotations.parquet]
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f429978f563/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f429978f563]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429978f563']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429978f563']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.49 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-compute-collect-immundata.R:   2.
  > test-compute-collect-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-agg-strata.R: v 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 [/tmp/Rtmpk8pKcU/file24f3f9617f3798/annotations.parquet]
  > 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: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f9617f3798/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f9617f3798]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9617f3798']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9617f3798']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.06 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpr0WkVU/file24f429230ea9f8/annotations.parquet]
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f429230ea9f8/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f429230ea9f8]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429230ea9f8']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429230ea9f8']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.19 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-barcodes.R:   2.
  > test-filter-barcodes.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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-barcodes.R: v Renaming is finished
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Preprocessing the data 
  > test-filter-barcodes.R:   1. exclude_columns
  > test-filter-barcodes.R:   2. filter_nonproductive
  > test-agg-strata.R: v 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 [/tmp/Rtmpk8pKcU/file24f3f91096e646/annotations.parquet]
  > 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: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f91096e646/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f91096e646]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f91096e646']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f91096e646']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.09 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Postprocessing the data 
  > test-filter-barcodes.R:   1. prefix_barcodes
  > test-filter-barcodes.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-barcodes.R: v Postprocessing plan is ready
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk 
  > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/file24f429a2051e/annotations.parquet]
  > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f429a2051e/metadata.json]
  > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f429a2051e]
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429a2051e']
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429a2051e']
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Summary 
  > test-filter-barcodes.R: i Time elapsed: 3.18 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-exact.R:   2.
  > test-filter-immundata-exact.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-exact.R: i Checking if all files are of the same type
  > test-filter-immundata-exact.R: v All files have the same extension
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Renaming the columns and schemas 
  > test-filter-immundata-exact.R: v Renaming is finished
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Preprocessing the data 
  > test-filter-immundata-exact.R:   1. exclude_columns
  > test-filter-immundata-exact.R:   2. filter_nonproductive
  > test-filter-immundata-exact.R: v Preprocessing plan is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Aggregating the data to receptors 
  > test-filter-immundata-exact.R: i No locus information found
  > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-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 [/tmp/Rtmpk8pKcU/file24f3f951e2f76f/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f951e2f76f/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f951e2f76f]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f951e2f76f']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f951e2f76f']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.2 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-exact.R: 
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > 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 [/tmp/Rtmpr0WkVU/file24f4294ff3c9f6/annotations.parquet]
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4294ff3c9f6/metadata.json]
  > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4294ff3c9f6]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4294ff3c9f6']
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4294ff3c9f6']
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Summary 
  > test-filter-immundata-exact.R: i Time elapsed: 3.26 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 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: 
  > test-filter-immundata-hamm.R: -- Reading repertoire data 
  > test-filter-immundata-hamm.R:   1.
  > test-filter-immundata-hamm.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-hamm.R:   2.
  > test-filter-immundata-hamm.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-hamm.R: i Checking if all files are of the same type
  > test-filter-immundata-hamm.R: v All files have the same extension
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Renaming the columns and schemas 
  > test-filter-immundata-hamm.R: v Renaming is finished
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Preprocessing the data 
  > test-filter-immundata-hamm.R:   1. exclude_columns
  > test-filter-immundata-hamm.R:   2. filter_nonproductive
  > test-filter-immundata-hamm.R: v Preprocessing plan is ready
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Aggregating the data to receptors 
  > test-filter-immundata-hamm.R: i No locus information found
  > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-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 [/tmp/Rtmpr0WkVU/file24f4295c1323cf/annotations.parquet]
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f91592883a/annotations.parquet]
  > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4295c1323cf/metadata.json]
  > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4295c1323cf]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4295c1323cf']
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4295c1323cf']
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Summary 
  > test-filter-immundata-hamm.R: i Time elapsed: 3.21 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: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f91592883a/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f91592883a]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f91592883a']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f91592883a']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.63 secs
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Reading repertoire data 
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-lev.R:   1.
  > test-filter-immundata-lev.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-lev.R:   2.
  > test-filter-immundata-lev.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-lev.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R: v All files have the same extension
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > test-filter-immundata-lev.R: v Renaming is finished
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Preprocessing the data 
  > test-filter-immundata-lev.R:   1. exclude_columns
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-agg-strata.R:   2.
  > test-agg-strata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-agg-strata.R: i Checking if all files are of the same type
  > test-agg-strata.R: v All files have the same extension
  > test-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Postprocessing the data 
  > test-filter-immundata-lev.R:   1. prefix_barcodes
  > test-filter-immundata-lev.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-lev.R: v Postprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/file24f42946d4ff8b/annotations.parquet]
  > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f42946d4ff8b/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f42946d4ff8b]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42946d4ff8b']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42946d4ff8b']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 3.27 secs
  > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: v 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-lev.R:   2.
  > test-filter-immundata-lev.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-lev.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R: v All files have the same extension
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > test-filter-immundata-lev.R: v Renaming is finished
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Preprocessing the data 
  > test-filter-immundata-lev.R:   1. exclude_columns
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-filter-immundata-lev.R: 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 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 [/tmp/Rtmpk8pKcU/file24f3f9277bb023/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f9277bb023/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f9277bb023]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9277bb023']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9277bb023']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.39 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-regex.R:   2.
  > test-filter-immundata-regex.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-regex.R: i Checking if all files are of the same type
  > test-filter-immundata-regex.R: v All files have the same extension
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Renaming the columns and schemas 
  > test-filter-immundata-regex.R: v Renaming is finished
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Preprocessing the data 
  > test-filter-immundata-regex.R:   1. exclude_columns
  > test-filter-immundata-regex.R:   2. filter_nonproductive
  > test-filter-immundata-regex.R: v Preprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Aggregating the data to receptors 
  > test-filter-immundata-regex.R: i No locus information found
  > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-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 [/tmp/Rtmpr0WkVU/file24f429523dc007/annotations.parquet]
  > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f429523dc007/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f429523dc007]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429523dc007']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f429523dc007']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 3.4 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata.R:   2.
  > test-filter-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata.R: i Checking if all files are of the same type
  > test-filter-immundata.R: v All files have the same extension
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: v Renaming is finished
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Preprocessing the data 
  > test-filter-immundata.R:   1. exclude_columns
  > test-filter-immundata.R:   2. filter_nonproductive
  > test-filter-immundata.R: v Preprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Aggregating the data to receptors 
  > test-filter-immundata.R: i No locus information found
  > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Postprocessing the data 
  > test-filter-immundata-regex.R:   1. prefix_barcodes
  > test-filter-immundata-regex.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-regex.R: v Postprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f95f300e5b/annotations.parquet]
  > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f95f300e5b/metadata.json]
  > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f95f300e5b]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f95f300e5b']
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f95f300e5b']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Summary 
  > test-filter-immundata-regex.R: i Time elapsed: 3.27 secs
  > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Reading repertoire data 
  > test-filter-receptors.R:   1.
  > test-filter-receptors.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-receptors.R:   2.
  > test-filter-receptors.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-receptors.R: i Checking if all files are of the same type
  > test-filter-receptors.R: v All files have the same extension
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Renaming the columns and schemas 
  > test-filter-receptors.R: v Renaming is finished
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Preprocessing the data 
  > test-filter-receptors.R:   1. exclude_columns
  > test-filter-receptors.R:   2. filter_nonproductive
  > test-filter-receptors.R: v Preprocessing plan is ready
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Aggregating the data to receptors 
  > test-filter-receptors.R: i No locus information found
  > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-immundata.R: v Joining plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Postprocessing the data 
  > test-filter-immundata.R:   1. prefix_barcodes
  > test-filter-immundata.R: v Postprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/file24f4293bb48b63/annotations.parquet]
  > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f4293bb48b63/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f4293bb48b63]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4293bb48b63']
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f4293bb48b63']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 4.16 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata.R:   2.
  > test-filter-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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 [/tmp/Rtmpk8pKcU/file24f3f9649f82a1/annotations.parquet]
  > test-filter-immundata.R: v Preprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Aggregating the data to receptors 
  > test-filter-immundata.R: i No locus information found
  > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-receptors.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f9649f82a1/metadata.json]
  > test-filter-receptors.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f9649f82a1]
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9649f82a1']
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f9649f82a1']
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Summary 
  > test-filter-receptors.R: i Time elapsed: 3.18 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/legacy_v1_24f3f97bbf761f/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/legacy_v1_24f3f97bbf761f/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/legacy_v1_24f3f97bbf761f]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/legacy_v1_24f3f97bbf761f']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/legacy_v1_24f3f97bbf761f']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.5 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/legacy_v1_24f3f97bbf761f']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Postprocessing the data 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-filter-immundata.R:   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 [/tmp/Rtmpr0WkVU/file24f42955cd4ffd/annotations.parquet]
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/file24f42955cd4ffd/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/file24f42955cd4ffd]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42955cd4ffd']
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/file24f42955cd4ffd']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 3.28 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. /tmp/Rtmpr0WkVU/file24f4296d93ecbf.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 [/tmp/Rtmpr0WkVU/test_immundata_24f4294da71a42/annotations.parquet]
  > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4294da71a42/metadata.json]
  > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4294da71a42]
  > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4294da71a42']
  > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4294da71a42']
  > test-io-repertoires-agg-stepwise.R: 
  > test-io-repertoires-agg-stepwise.R: -- Summary 
  > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.3 secs
  > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors
  > 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.45 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. /tmp/Rtmpr0WkVU/file24f42919e99056.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 [/tmp/Rtmpr0WkVU/test_immundata_24f4296bedb770/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4296bedb770/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4296bedb770]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4296bedb770']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4296bedb770']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.22 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. /tmp/Rtmpr0WkVU/file24f4292cd78e2d.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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f42979d64040/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.47 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpr0WkVU/test_immundata_24f42979d64040/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42979d64040]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42979d64040']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42979d64040']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.81 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: 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. /tmp/Rtmpr0WkVU/file24f42974bc4ab9.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 [/tmp/Rtmpr0WkVU/test_immundata_24f42931e16bc0/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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f42931e16bc0/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42931e16bc0]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42931e16bc0']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42931e16bc0']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.96 secs
  > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.43 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: Rows: 2 Columns: 4
  > test-io-immundata.R: -- Column specification --------------------------------------------------------
  > test-io-immundata.R: Delimiter: "\t"
  > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix
  > test-io-immundata.R: 
  > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-io-immundata.R: v Metadata parsed successfully
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. /tmp/Rtmpr0WkVU/file24f42935661cc9.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-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > 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 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 [/tmp/Rtmpr0WkVU/test_immundata_24f4293fa04bd0/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4293fa04bd0/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4293fa04bd0]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4293fa04bd0']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4293fa04bd0']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.9 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. /tmp/Rtmpr0WkVU/file24f42913f8b09e.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 [/tmp/Rtmpr0WkVU/test_immundata_24f4292aad68c1/annotations.parquet]
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4292aad68c1/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4292aad68c1]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4292aad68c1']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4292aad68c1']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.09 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. /tmp/Rtmpr0WkVU/file24f4291e8e9b37.tsv
  > test-io-repertoires-agg.R: i Checking if all files are of the same type
  > test-io-repertoires-agg.R: v All files have the same extension
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Renaming the columns and schemas 
  > test-io-repertoires-agg.R: v Renaming is finished
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Preprocessing the data 
  > test-io-repertoires-agg.R:   1. exclude_columns
  > test-io-repertoires-agg.R:   2. filter_nonproductive
  > test-io-repertoires-agg.R:   ! No columns with the productive specification found; skipping the filtering
  > test-io-repertoires-agg.R: v Preprocessing plan is ready
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Aggregating the data to receptors 
  > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-immundata.R: v 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 3.45 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- 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 [/tmp/Rtmpr0WkVU/test_immundata_24f4292ba807f0/annotations.parquet]
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4292ba807f0/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4292ba807f0]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4292ba807f0']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4292ba807f0']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 1.11 secs
  > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-repertoires-counts.R:   1. /tmp/Rtmpr0WkVU/file24f42945cae166.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 [/tmp/Rtmpr0WkVU/test_immundata_24f429532f6dd0/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429532f6dd0/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429532f6dd0]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429532f6dd0']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429532f6dd0']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.25 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. /tmp/Rtmpr0WkVU/file24f429df9f332.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f4297f9ac45d/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4297f9ac45d/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4297f9ac45d]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297f9ac45d']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297f9ac45d']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.26 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. /tmp/Rtmpr0WkVU/file24f4297b1c6a60.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.42 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f42955647ee0/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f42955647ee0/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42955647ee0]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42955647ee0']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42955647ee0']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.92 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-repertoires-counts.R:   1. /tmp/Rtmpr0WkVU/file24f429370575f2.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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/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-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f429b6c40b6/annotations.parquet]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.44 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429b6c40b6/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429b6c40b6]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002']
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429b6c40b6']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429b6c40b6']
  > test-io-repertoires-counts.R: 
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json]
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.93 secs
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/treated/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/treated/v001']
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/metadata.json]
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectB']
  > test-io-repertoires-counts.R:   1. /tmp/Rtmpr0WkVU/file24f4292bed9a9b.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: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f4297b332fd7/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4297b332fd7/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4297b332fd7]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297b332fd7']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297b332fd7']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.9 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")]
  > 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. /tmp/Rtmpr0WkVU/file24f4297c8ecf6f.tsv
  > test-io-repertoires-counts.R: i Checking if all files are of the same type
  > test-io-repertoires-counts.R: v All files have the same extension
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.51 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v002']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/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 ['/tmp/Rtmpk8pKcU/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f4291bbbef9c/annotations.parquet]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4291bbbef9c/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4291bbbef9c]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4291bbbef9c']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4291bbbef9c']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.08 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|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. /tmp/Rtmpr0WkVU/file24f429b2b4bab.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 [/tmp/Rtmpr0WkVU/test_immundata_24f429469f830e/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429469f830e/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429469f830e]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429469f830e']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429469f830e']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 0.16 secs
  > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Reading repertoire data 
  > test-io-repertoires-counts.R:   1. /tmp/Rtmpr0WkVU/file24f42934ca7477.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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f429283ed975/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.49 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429283ed975/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429283ed975]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429283ed975']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429283ed975']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.01 secs
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001']
  > 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. /tmp/Rtmpr0WkVU/file24f42934ca7477.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: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f429517389ad/annotations.parquet]
  > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429517389ad/metadata.json]
  > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429517389ad]
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429517389ad']
  > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429517389ad']
  > test-io-repertoires-counts.R: 
  > test-io-repertoires-counts.R: -- Summary 
  > test-io-repertoires-counts.R: i Time elapsed: 1.05 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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 [/tmp/Rtmpr0WkVU/test_immundata_24f42962ac9c38/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f42962ac9c38/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42962ac9c38]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42962ac9c38']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42962ac9c38']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 1.59 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 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-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > 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 [/tmp/Rtmpk8pKcU/file24f3f941c0d4e8/annotations.parquet]
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f941c0d4e8/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f941c0d4e8]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f941c0d4e8']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f941c0d4e8']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 3.27 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.53 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectB']
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/baseline/v001']
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectB']
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectB/snapshots/baseline/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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: 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 [/tmp/Rtmpr0WkVU/test_immundata_24f42946e82898/annotations.parquet]
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f42946e82898/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42946e82898]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42946e82898']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42946e82898']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.08 secs
  > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Reading repertoire data 
  > test-io-repertoires-files.R:   1.
  > test-io-repertoires-files.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.56 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 [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/ops/v001]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/imd_snap_tests/projectA/snapshots/ops/v001']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Reading repertoire data 
  > test-io-immundata.R:   1.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-immundata.R: i Checking if all files are of the same type
  > test-io-immundata.R: v All files have the same extension
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Renaming the columns and schemas 
  > test-io-immundata.R: v Renaming is finished
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Preprocessing the data 
  > test-io-immundata.R:   1. exclude_columns
  > test-io-immundata.R:   2. filter_nonproductive
  > test-io-immundata.R: v Preprocessing plan is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Aggregating the data to receptors 
  > test-io-immundata.R: i No locus information found
  > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f4297a5b3119/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4297a5b3119/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4297a5b3119]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297a5b3119']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297a5b3119']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.06 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Postprocessing the data 
  > test-io-immundata.R:   1. prefix_barcodes
  > test-io-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-immundata.R: v Postprocessing plan is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f926df9e2e/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f926df9e2e/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f926df9e2e]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f926df9e2e']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f926df9e2e']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 3.27 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-immundata.R:   2.
  > test-io-immundata.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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 [/tmp/Rtmpr0WkVU/test_immundata_24f429505569c6/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429505569c6/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429505569c6]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429505569c6']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429505569c6']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.59 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Postprocessing the data 
  > test-io-immundata.R:   1. prefix_barcodes
  > test-io-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-immundata.R: v Postprocessing plan is ready
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/file24f3f93fab6fc3/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/file24f3f93fab6fc3/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/file24f3f93fab6fc3]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f93fab6fc3']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/file24f3f93fab6fc3']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 3.43 secs
  > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Reading repertoire data 
  > test-io-repertoires-processing.R:   1.
  > test-io-repertoires-processing.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-processing.R: i Checking if all files are of the same type
  > test-io-repertoires-processing.R: v All files have the same extension
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Renaming the columns and schemas 
  > test-io-repertoires-processing.R: v Renaming is finished
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Preprocessing the data 
  > test-io-repertoires-processing.R:   1. exclude_columns
  > test-io-repertoires-processing.R: v Preprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Postprocessing the data 
  > test-io-repertoires-processing.R:   1. prefix_barcodes
  > test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires-processing.R: v Postprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/test-exclude/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test-exclude/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test-exclude]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-exclude']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-exclude']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.67 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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 [/tmp/Rtmpr0WkVU/test_immundata_24f429ed9ac3/annotations.parquet]
  > test-io-repertoires-processing.R: v Preprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f429ed9ac3/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f429ed9ac3]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429ed9ac3']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f429ed9ac3']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.65 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-files.R:   2.
  > test-io-repertoires-files.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-files.R: i Checking if all files are of the same type
  > test-io-repertoires-files.R: v All files have the same extension
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Renaming the columns and schemas 
  > test-io-repertoires-files.R: v Renaming is finished
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Aggregating the data to receptors 
  > test-io-repertoires-files.R: i No locus information found
  > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Postprocessing the data 
  > test-io-repertoires-processing.R:   1. prefix_barcodes
  > test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires-processing.R: v Postprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/test-rename/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test-rename/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test-rename]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-rename']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-rename']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.83 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires-processing.R: i Checking if all files are of the same type
  > test-io-repertoires-processing.R: v All files have the same extension
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Renaming the columns and schemas 
  > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene
  > test-io-repertoires-processing.R: v Renaming is finished
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Preprocessing the data 
  > test-io-repertoires-processing.R:   1. exclude_columns
  > test-io-repertoires-processing.R: v Preprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Postprocessing the data 
  > test-io-repertoires-processing.R:   1. prefix_barcodes
  > test-io-repertoires-processing.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires-processing.R: v Postprocessing plan is ready
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/Rtmpk8pKcU/test-exclude-rename/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test-exclude-rename/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test-exclude-rename]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-exclude-rename']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-exclude-rename']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 1.62 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-files.R: v Joining plan is ready
  > test-io-repertoires-processing.R: -- Aggregating the data to receptors 
  > test-io-repertoires-processing.R: i No locus information found
  > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f42947cae59d/annotations.parquet]
  > test-io-repertoires-files.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f42947cae59d/metadata.json]
  > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42947cae59d]
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42947cae59d']
  > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42947cae59d']
  > test-io-repertoires-files.R: 
  > test-io-repertoires-files.R: -- Summary 
  > test-io-repertoires-files.R: i Time elapsed: 3.57 secs
  > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Reading repertoire data 
  > test-io-repertoires-schema-paired.R:   1.
  > test-io-repertoires-schema-paired.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet]
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Reading repertoire data 
  > test-io-repertoires-processing.R:   1.
  > test-io-repertoires-processing.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet]
  > 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-processing.R:   2.
  > test-io-repertoires-processing.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-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 [/tmp/Rtmpk8pKcU/test_immundata_24f3f981e3e76/annotations.parquet]
  > 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 [/tmp/Rtmpr0WkVU/test_immundata_24f4296343de71/annotations.parquet]
  > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test_immundata_24f3f981e3e76/metadata.json]
  > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test_immundata_24f3f981e3e76]
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f981e3e76']
  > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f981e3e76']
  > test-io-repertoires-processing.R: 
  > test-io-repertoires-processing.R: -- Summary 
  > test-io-repertoires-processing.R: i Time elapsed: 18.18 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
  Saving _problems/test-io-repertoires-processing-90.R
  Saving _problems/test-io-repertoires-processing-110.R
  > 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz
  > test-io-repertoires-schema-single.R: i Checking if all files are of the same type
  > test-io-repertoires-schema-single.R: v All files have the same extension
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors 
  > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only
  > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4296343de71/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4296343de71]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4296343de71']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4296343de71']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 22.44 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz
  > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type
  > test-io-repertoires-schema-paired.R: v All files have the same extension
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors 
  > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only
  > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible
  > test-io-repertoires-schema-single.R: 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 [/tmp/Rtmpk8pKcU/test_immundata_24f3f91d224f6c/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test_immundata_24f3f91d224f6c/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test_immundata_24f3f91d224f6c]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f91d224f6c']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f91d224f6c']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 3.83 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. /tmp/Rtmpk8pKcU/file24f3f9797d5461.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 [/tmp/Rtmpk8pKcU/test_immundata_24f3f96b609a19/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test_immundata_24f3f96b609a19/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test_immundata_24f3f96b609a19]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f96b609a19']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f96b609a19']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 0.29 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. /tmp/Rtmpk8pKcU/file24f3f937f837c9.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 [/tmp/Rtmpk8pKcU/test_immundata_24f3f933d2a245/annotations.parquet]
  > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test_immundata_24f3f933d2a245/metadata.json]
  > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test_immundata_24f3f933d2a245]
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f933d2a245']
  > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test_immundata_24f3f933d2a245']
  > test-io-repertoires-schema-single.R: 
  > test-io-repertoires-schema-single.R: -- Summary 
  > test-io-repertoires-schema-single.R: i Time elapsed: 0.31 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 [/tmp/Rtmpk8pKcU/test-no-barcodes/annotations.parquet]
  > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/Rtmpk8pKcU/test-no-barcodes/metadata.json]
  > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/Rtmpk8pKcU/test-no-barcodes]
  > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/test-no-barcodes']
  > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/Rtmpk8pKcU/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: 1.75 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires-schema.R: i Checking if all files are of the same type
  > test-io-repertoires-schema.R: v All files have the same extension
  > test-io-repertoires-schema.R: 
  > test-io-repertoires-schema.R: -- Renaming the columns and schemas 
  > test-io-repertoires-schema.R: v Renaming is finished
  > test-io-repertoires-schema.R: 
  > test-io-repertoires-schema.R: -- Preprocessing the data 
  > test-io-repertoires-schema.R:   1. exclude_columns
  > test-io-repertoires-schema.R:   2. filter_nonproductive
  > test-io-repertoires-schema.R: v Preprocessing plan is ready
  > test-io-repertoires-schema.R: 
  > test-io-repertoires-schema.R: -- Aggregating the data to receptors 
  > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/Rtmpr0WkVU/test_immundata_24f42932437d17/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f42932437d17/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f42932437d17]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42932437d17']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f42932437d17']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 23.85 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. /tmp/Rtmpr0WkVU/file24f42923e4ee56.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 [/tmp/Rtmpr0WkVU/test_immundata_24f4297bfbba0b/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4297bfbba0b/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4297bfbba0b]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297bfbba0b']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4297bfbba0b']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 1.44 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. /tmp/Rtmpr0WkVU/file24f42913f33676.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 [/tmp/Rtmpr0WkVU/test_immundata_24f4294640f306/annotations.parquet]
  > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/Rtmpr0WkVU/test_immundata_24f4294640f306/metadata.json]
  > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/Rtmpr0WkVU/test_immundata_24f4294640f306]
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4294640f306']
  > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/Rtmpr0WkVU/test_immundata_24f4294640f306']
  > test-io-repertoires-schema-paired.R: 
  > test-io-repertoires-schema-paired.R: -- Summary 
  > test-io-repertoires-schema-paired.R: i Time elapsed: 1.27 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 2 | WARN 0 | SKIP 0 | PASS 349 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ──
  Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"}
  Backtrace:
       ▆
    1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3
    2. │ └─immundata:::write_immundata_internal(...)
    3. │   ├─duckplyr::compute_parquet(...)
    4. │   └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options)
    5. │     └─duckdb$rel_to_parquet(rel, path, options)
    6. │       └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options)
    7. │         ├─rlang::try_fetch(...)
    8. │         │ ├─base::tryCatch(...)
    9. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12. │         │ └─base::withCallingHandlers(...)
   13. │         └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps)
   14. └─base::.handleSimpleError(...)
   15.   └─rlang (local) h(simpleError(msg, call))
   16.     └─handlers[[1L]](cnd)
   17.       └─duckdb:::rethrow_error_from_rapi(e, call)
   18.         └─rlang::abort(msg, call = call)
  ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ──
  Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"}
  Backtrace:
       ▆
    1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3
    2. │ └─immundata:::write_immundata_internal(...)
    3. │   ├─duckplyr::compute_parquet(...)
    4. │   └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options)
    5. │     └─duckdb$rel_to_parquet(rel, path, options)
    6. │       └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options)
    7. │         ├─rlang::try_fetch(...)
    8. │         │ ├─base::tryCatch(...)
    9. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12. │         │ └─base::withCallingHandlers(...)
   13. │         └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps)
   14. └─base::.handleSimpleError(...)
   15.   └─rlang (local) h(simpleError(msg, call))
   16.     └─handlers[[1L]](cnd)
   17.       └─duckdb:::rethrow_error_from_rapi(e, call)
   18.         └─rlang::abort(msg, call = call)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ]
  Error:
  ! Test failures.
  Execution halted