Running ‘testthat.R’ [159s/79s]
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-agg-strata.R: 
  > test-annotate-barcodes.R: v Renaming is finished
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Preprocessing the data 
  > test-annotate-barcodes.R:   1. exclude_columns
  > test-annotate-barcodes.R:   2. filter_nonproductive
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-annotate-barcodes.R: v Preprocessing plan is ready
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Aggregating the data to receptors 
  > test-annotate-barcodes.R: i No locus information found
  > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Postprocessing the data 
  > test-annotate-barcodes.R:   1. prefix_barcodes
  > test-annotate-barcodes.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-barcodes.R: v Postprocessing plan is ready
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmppODfWT/file379ffe6e57dcc2/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/RtmppODfWT/file379ffe6e57dcc2/metadata.json]
  > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe6e57dcc2]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe6e57dcc2']
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe6e57dcc2']
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Summary 
  > test-annotate-barcodes.R: i Time elapsed: 3.35 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/Rtmpipmm72/file379fe2682ef5ca/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe2682ef5ca/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe2682ef5ca]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe2682ef5ca']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe2682ef5ca']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.35 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-annotate-external.R: 
  > test-annotate-external.R: -- Renaming the columns and schemas 
  > 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 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/Rtmpipmm72/file379fe262909efc/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe262909efc/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe262909efc]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe262909efc']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe262909efc']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.95 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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/RtmppODfWT/file379ffe77e67e61/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe77e67e61/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe77e67e61]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe77e67e61']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe77e67e61']
  > 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-annotate-external.R: v Preprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Aggregating the data to receptors 
  > test-annotate-external.R: i No locus information found
  > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe262f32735/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe262f32735/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe262f32735]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe262f32735']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe262f32735']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.11 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Postprocessing the data 
  > test-annotate-external.R:   1. prefix_barcodes
  > test-annotate-external.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-external.R: v Postprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmppODfWT/file379ffe69477332/annotations.parquet]
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > test-agg-strata.R:   /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-annotate-external.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe69477332/metadata.json]
  > test-agg-strata.R:   2. filter_nonproductive
  > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe69477332]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe69477332']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe69477332']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.06 secs
  > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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 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: -- 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-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/RtmppODfWT/file379ffe6a9c4aa8/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-annotate-external.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe6a9c4aa8/metadata.json]
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe276d53407/annotations.parquet]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe6a9c4aa8]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe6a9c4aa8']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe6a9c4aa8']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.07 secs
  > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Reading repertoire data 
  > test-annotate-external.R:   1.
  > 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-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe276d53407/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe276d53407]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe276d53407']
  > test-annotate-external.R:   2. filter_nonproductive
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe276d53407']
  > 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-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-annotate-external.R: v Preprocessing plan is ready
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Aggregating the data to receptors 
  > test-annotate-external.R: i No locus information found
  > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > 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/RtmppODfWT/file379ffe76c1f6b4/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe76c1f6b4/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe76c1f6b4]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe76c1f6b4']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe76c1f6b4']
  > 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-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-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 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/Rtmpipmm72/file379fe24e866a12/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe24e866a12/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe24e866a12]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe24e866a12']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe24e866a12']
  > 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-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/RtmppODfWT/file379ffe9077ad1/annotations.parquet]
  > test-annotate-external.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe9077ad1/metadata.json]
  > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe9077ad1]
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe9077ad1']
  > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe9077ad1']
  > test-annotate-external.R: 
  > test-annotate-external.R: -- Summary 
  > test-annotate-external.R: i Time elapsed: 3.1 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-annotate-receptors.R: v Preprocessing plan is ready
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Aggregating the data to receptors 
  > test-annotate-receptors.R: i No locus information found
  > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe24b885a4a/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe24b885a4a/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe24b885a4a]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe24b885a4a']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe24b885a4a']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 3.98 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/RtmppODfWT/file379ffe2055a0cd/annotations.parquet]
  > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe2055a0cd/metadata.json]
  > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe2055a0cd]
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe2055a0cd']
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe2055a0cd']
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Summary 
  > test-annotate-receptors.R: i Time elapsed: 3.13 secs
  > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-compute-collect-immundata.R: Rows: 2 Columns: 4
  > test-compute-collect-immundata.R: -- Column specification --------------------------------------------------------
  > test-compute-collect-immundata.R: Delimiter: "\t"
  > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-compute-collect-immundata.R: v Metadata parsed successfully
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Reading repertoire data 
  > test-compute-collect-immundata.R:   1.
  > 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-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-compute-collect-immundata.R: v Postprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmppODfWT/file379ffe1038f3cc/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe1038f3cc/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe1038f3cc]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe1038f3cc']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe1038f3cc']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.16 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-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the 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:   1. prefix_barcodes
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe219021b93/annotations.parquet]
  > test-compute-collect-immundata.R: v Renaming is finished
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Preprocessing the data 
  > test-compute-collect-immundata.R:   1. exclude_columns
  > test-compute-collect-immundata.R:   2. filter_nonproductive
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe219021b93/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe219021b93]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe219021b93']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe219021b93']
  > 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: v Preprocessing plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Aggregating the data to receptors 
  > test-compute-collect-immundata.R: i No locus information found
  > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > 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-compute-collect-immundata.R: v Joining plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Postprocessing the data 
  > test-compute-collect-immundata.R:   1. prefix_barcodes
  > test-agg-strata.R: v 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 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/RtmppODfWT/file379ffe7e6eda06/annotations.parquet]
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe7e6eda06/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe7e6eda06]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe7e6eda06']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe7e6eda06']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.59 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: 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/Rtmpipmm72/file379fe2723c6da3/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe2723c6da3/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe2723c6da3]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe2723c6da3']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe2723c6da3']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.18 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Reading repertoire data 
  > test-agg-strata.R:   1.
  > 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-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/RtmppODfWT/file379ffe55312a2c/annotations.parquet]
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe55312a2c/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe55312a2c]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe55312a2c']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe55312a2c']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.4 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: 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/Rtmpipmm72/file379fe295f0968/annotations.parquet]
  > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe295f0968/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe295f0968]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe295f0968']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe295f0968']
  > 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-agg-strata.R: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-compute-collect-immundata.R: v Joining plan is ready
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Postprocessing the data 
  > test-compute-collect-immundata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-compute-collect-immundata.R: v 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/RtmppODfWT/file379ffe1f575c03/annotations.parquet]
  > test-agg-strata.R: v Preprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Aggregating the data to receptors 
  > test-agg-strata.R: i No locus information found
  > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe1f575c03/metadata.json]
  > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe1f575c03]
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe1f575c03']
  > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe1f575c03']
  > test-compute-collect-immundata.R: 
  > test-compute-collect-immundata.R: -- Summary 
  > test-compute-collect-immundata.R: i Time elapsed: 4.22 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-filter-barcodes.R: v Renaming is finished
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Preprocessing the data 
  > test-filter-barcodes.R:   1. exclude_columns
  > test-filter-barcodes.R:   2. filter_nonproductive
  > test-filter-barcodes.R: v Preprocessing plan is ready
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Aggregating the data to receptors 
  > test-filter-barcodes.R: i No locus information found
  > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-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/RtmppODfWT/file379ffeb8809cc/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/Rtmpipmm72/file379fe21cd72efa/annotations.parquet]
  > test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffeb8809cc/metadata.json]
  > test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffeb8809cc]
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffeb8809cc']
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffeb8809cc']
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Summary 
  > test-filter-barcodes.R: i Time elapsed: 3.02 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-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe21cd72efa/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe21cd72efa]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe21cd72efa']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe21cd72efa']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.19 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-exact.R: 
  > 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-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-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 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-exact.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Postprocessing the data 
  > test-filter-immundata-exact.R:   1. prefix_barcodes
  > test-filter-immundata-exact.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-exact.R: v Postprocessing plan is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/RtmppODfWT/file379ffe4f085d67/annotations.parquet]
  > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe4f085d67/metadata.json]
  > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe4f085d67]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe4f085d67']
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe4f085d67']
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Summary 
  > test-filter-immundata-exact.R: i Time elapsed: 3.12 secs
  > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Reading repertoire data 
  > test-filter-immundata-hamm.R:   1.
  > 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-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-filter-immundata-hamm.R: 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 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/Rtmpipmm72/file379fe2647ea159/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe2647ea159/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe2647ea159]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe2647ea159']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe2647ea159']
  > 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-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-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/RtmppODfWT/file379ffe4a26c15b/annotations.parquet]
  > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe4a26c15b/metadata.json]
  > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe4a26c15b]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe4a26c15b']
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe4a26c15b']
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Summary 
  > test-filter-immundata-hamm.R: i Time elapsed: 3.11 secs
  > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Reading repertoire data 
  > test-filter-immundata-lev.R:   1.
  > 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-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-agg-strata.R: v Postprocessing plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Saving the newly created ImmunData to disk 
  > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe248cdde54/annotations.parquet]
  > test-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe248cdde54/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe248cdde54]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe248cdde54']
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe248cdde54']
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Summary 
  > test-agg-strata.R: i Time elapsed: 4.27 secs
  > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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/RtmppODfWT/file379ffe39f8a4d8/annotations.parquet]
  > test-agg-strata.R: Rows: 2 Columns: 4
  > test-agg-strata.R: -- Column specification --------------------------------------------------------
  > test-agg-strata.R: Delimiter: "\t"
  > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix
  > test-agg-strata.R: 
  > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-agg-strata.R: v Metadata parsed successfully
  > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe39f8a4d8/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe39f8a4d8]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe39f8a4d8']
  > 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-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe39f8a4d8']
  > test-agg-strata.R: v All files have the same extension
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 3.09 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: 
  > test-agg-strata.R: -- Renaming the columns and schemas 
  > test-agg-strata.R: v Renaming is finished
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Preprocessing the data 
  > test-agg-strata.R:   1. exclude_columns
  > test-agg-strata.R:   2. filter_nonproductive
  > test-filter-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-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:   2. filter_nonproductive
  > test-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-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/RtmppODfWT/file379ffe60fb4b3c/annotations.parquet]
  > test-agg-strata.R: v Joining plan is ready
  > test-agg-strata.R: 
  > test-agg-strata.R: -- Postprocessing the data 
  > test-agg-strata.R:   1. prefix_barcodes
  > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe60fb4b3c/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe60fb4b3c]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe60fb4b3c']
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe60fb4b3c']
  > 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 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/Rtmpipmm72/file379fe26a479853/annotations.parquet]
  > 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-agg-strata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe26a479853/metadata.json]
  > test-agg-strata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe26a479853]
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe26a479853']
  > test-filter-immundata-regex.R:   1. exclude_columns
  > test-agg-strata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe26a479853']
  > 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-filter-immundata-regex.R:   2. filter_nonproductive
  > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-filter-immundata-regex.R: v Preprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Aggregating the data to receptors 
  > test-filter-immundata-regex.R: i No locus information found
  > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: Rows: 2 Columns: 4
  > test-filter-immundata.R: -- Column specification --------------------------------------------------------
  > test-filter-immundata.R: Delimiter: "\t"
  > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
  > test-filter-immundata.R: 
  > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-filter-immundata.R: v Metadata parsed successfully
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Reading repertoire data 
  > test-filter-immundata.R:   1.
  > 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/RtmppODfWT/file379ffe67813d42/annotations.parquet]
  > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe67813d42/metadata.json]
  > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe67813d42]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe67813d42']
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe67813d42']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Summary 
  > test-filter-immundata-regex.R: i Time elapsed: 3.11 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-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-receptors.R: v Preprocessing plan is ready
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Aggregating the data to receptors 
  > test-filter-receptors.R: i No locus information found
  > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: v Joining plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Postprocessing the data 
  > test-filter-immundata.R:   1. prefix_barcodes
  > test-filter-immundata.R: v Postprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe22a0cc164/annotations.parquet]
  > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe22a0cc164/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe22a0cc164]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe22a0cc164']
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe22a0cc164']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 4.18 secs
  > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors
  > test-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-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/RtmppODfWT/file379ffe6ff40859/annotations.parquet]
  > test-filter-receptors.R: i Writing the metadata to [/tmp/RtmppODfWT/file379ffe6ff40859/metadata.json]
  > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmppODfWT/file379ffe6ff40859]
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe6ff40859']
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/file379ffe6ff40859']
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Summary 
  > test-filter-receptors.R: i Time elapsed: 3.26 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/RtmppODfWT/legacy_v1_379ffe666c6b87/annotations.parquet]
  > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Postprocessing the data 
  > test-filter-immundata.R:   1. prefix_barcodes
  > test-filter-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata.R: v Postprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpipmm72/file379fe22f3aad73/annotations.parquet]
  > test-io-immundata.R: i Writing the metadata to [/tmp/RtmppODfWT/legacy_v1_379ffe666c6b87/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmppODfWT/legacy_v1_379ffe666c6b87]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/legacy_v1_379ffe666c6b87']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/legacy_v1_379ffe666c6b87']
  > test-io-immundata.R: 
  > test-io-immundata.R: -- Summary 
  > test-io-immundata.R: i Time elapsed: 1.52 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/RtmppODfWT/legacy_v1_379ffe666c6b87']
  > 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-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpipmm72/file379fe22f3aad73/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpipmm72/file379fe22f3aad73]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe22f3aad73']
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/file379fe22f3aad73']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 3.27 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/Rtmpipmm72/file379fe22d908556.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/Rtmpipmm72/test_immundata_379fe2363cb34d/annotations.parquet]
  > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/Rtmpipmm72/test_immundata_379fe2363cb34d/metadata.json]
  > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/Rtmpipmm72/test_immundata_379fe2363cb34d]
  > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/test_immundata_379fe2363cb34d']
  > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/test_immundata_379fe2363cb34d']
  > test-io-repertoires-agg-stepwise.R: 
  > test-io-repertoires-agg-stepwise.R: -- Summary 
  > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.29 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
  Saving _problems/test-io-repertoires-agg-stepwise-125.R
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Reading repertoire data 
  > test-io-repertoires-agg.R:   1. /tmp/Rtmpipmm72/file379fe2698eebdd.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-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/RtmppODfWT/imd_snap_tests/projectA/annotations.parquet]
  > 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/Rtmpipmm72/test_immundata_379fe262e78667/annotations.parquet]
  > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/Rtmpipmm72/test_immundata_379fe262e78667/metadata.json]
  > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/Rtmpipmm72/test_immundata_379fe262e78667]
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/test_immundata_379fe262e78667']
  > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/Rtmpipmm72/test_immundata_379fe262e78667']
  > test-io-repertoires-agg.R: 
  > test-io-repertoires-agg.R: -- Summary 
  > test-io-repertoires-agg.R: i Time elapsed: 0.28 secs
  > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH]
  > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors
  > test-io-immundata.R: i Writing the metadata to [/tmp/RtmppODfWT/imd_snap_tests/projectA/metadata.json]
  > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmppODfWT/imd_snap_tests/projectA]
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/imd_snap_tests/projectA']
  > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmppODfWT/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: 
  > 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:  *** caught segfault ***
  > test-io-repertoires-agg.R: address (nil), cause 'unknown'
  
  Error:
  ! testthat subprocess exited in file 'test-io-repertoires-agg.R'.
  Caused by error:
  ! R session crashed with exit code -11
  Backtrace:
       ▆
    1. └─testthat::test_check("immundata")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files_parallel(...)
    5.         ├─withr::with_dir(...)
    6.         │ └─base::force(code)
    7.         ├─testthat::with_reporter(...)
    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.         └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
   13.           └─queue$poll(Inf)
   14.             └─base::lapply(...)
   15.               └─testthat (local) FUN(X[[i]], ...)
   16.                 └─private$handle_error(msg, i)
   17.                   └─cli::cli_abort(...)
   18.                     └─rlang::abort(...)
  Execution halted