* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck’
* using R Under development (unstable) (2026-03-10 r89593)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-03-11 04:24:54 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘immundata/DESCRIPTION’ ... OK
* this is package ‘immundata’ version ‘0.0.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘immundata’ can be installed ... [21s/70s] OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/12s] OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/14s] OK
* checking loading without being on the library search path ... [5s/16s] OK
* checking whether startup messages can be suppressed ... [5s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [25s/58s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [5s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [150s/310s]
 [151s/312s] ERROR
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: 5.
  → 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 0.0.5
  > 
  > 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:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-barcodes.R:   2.
  > test-annotate-barcodes.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-barcodes.R: i Checking if all files are of the same type
  > test-annotate-barcodes.R: v All files have the same extension
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Renaming the columns and schemas 
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Reading repertoire data 
  > test-annotate-barcodes.R: v Renaming is finished
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Preprocessing the data 
  > test-annotate-barcodes.R:   1. exclude_columns
  > test-annotate-receptors.R:   1.
  > test-annotate-receptors.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-annotate-receptors.R:   2.
  > test-annotate-receptors.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-annotate-receptors.R: i Checking if all files are of the same type
  > test-annotate-receptors.R: v All files have the same extension
  > test-annotate-barcodes.R:   2. filter_nonproductive
  > 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-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-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-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/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f5355076039/annotations.parquet]
  > 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/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a1015d0e/annotations.parquet]
  > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f5355076039/metadata.json]
  > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f5355076039]
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f5355076039']
  > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f5355076039']
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Summary 
  > test-annotate-receptors.R: i Time elapsed: 24.37 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
  > test-annotate-barcodes.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a1015d0e/metadata.json]
  > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a1015d0e]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a1015d0e']
  > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a1015d0e']
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Summary 
  > test-annotate-barcodes.R: i Time elapsed: 27.53 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
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Reading repertoire data 
  > test-filter-barcodes.R:   1.
  > test-filter-barcodes.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-barcodes.R:   2.
  > test-filter-barcodes.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-barcodes.R: i Checking if all files are of the same type
  > test-filter-barcodes.R: v All files have the same extension
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Renaming the columns and schemas 
  > test-filter-barcodes.R: v Renaming is finished
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Preprocessing the data 
  > test-filter-barcodes.R:   1. exclude_columns
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Reading repertoire data 
  > test-filter-immundata-exact.R:   1.
  > test-filter-immundata-exact.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-exact.R:   2.
  > test-filter-immundata-exact.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-exact.R: i Checking if all files are of the same type
  > test-filter-immundata-exact.R: v All files have the same extension
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Renaming the columns and schemas 
  > test-filter-barcodes.R:   2. filter_nonproductive
  > 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-barcodes.R: v Preprocessing plan is ready
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Aggregating the data to receptors 
  > test-filter-barcodes.R: i No locus information found
  > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-exact.R:   2. filter_nonproductive
  > test-filter-immundata-exact.R: v Preprocessing plan is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Aggregating the data to receptors 
  > test-filter-immundata-exact.R: i No locus information found
  > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-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/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f53690f78d0/annotations.parquet]
  > test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f53690f78d0/metadata.json]
  > test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f53690f78d0]
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f53690f78d0']
  > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f53690f78d0']
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Summary 
  > test-filter-barcodes.R: i Time elapsed: 23.48 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
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Reading repertoire data 
  > test-filter-immundata-hamm.R:   1.
  > test-filter-immundata-hamm.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-hamm.R:   2.
  > test-filter-immundata-hamm.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-hamm.R: i Checking if all files are of the same type
  > test-filter-immundata-hamm.R: v All files have the same extension
  > test-filter-immundata-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-hamm.R: 
  > test-filter-immundata-hamm.R: -- Renaming the columns and schemas 
  > 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/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7b15ada4/annotations.parquet]
  > test-filter-immundata-hamm.R: v Renaming is finished
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Preprocessing the data 
  > test-filter-immundata-hamm.R:   1. exclude_columns
  > test-filter-immundata-hamm.R:   2. filter_nonproductive
  > test-filter-immundata-hamm.R: v Preprocessing plan is ready
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Aggregating the data to receptors 
  > test-filter-immundata-hamm.R: i No locus information found
  > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7b15ada4/metadata.json]
  > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7b15ada4]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7b15ada4']
  > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7b15ada4']
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Summary 
  > test-filter-immundata-exact.R: i Time elapsed: 27.8 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
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Reading repertoire data 
  > test-filter-immundata-lev.R:   1.
  > test-filter-immundata-lev.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-lev.R:   2.
  > test-filter-immundata-lev.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-lev.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R: v All files have the same extension
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > test-filter-immundata-lev.R: v Renaming is finished
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Preprocessing the data 
  > test-filter-immundata-lev.R:   1. exclude_columns
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-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/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f535927f284/annotations.parquet]
  > 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/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a108cef87/annotations.parquet]
  > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f535927f284/metadata.json]
  > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f535927f284]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f535927f284']
  > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f535927f284']
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Summary 
  > test-filter-immundata-hamm.R: i Time elapsed: 27.2 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
  > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a108cef87/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a108cef87]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a108cef87']
  > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a108cef87']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 21.51 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
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Reading repertoire data 
  > test-filter-immundata-regex.R:   1.
  > test-filter-immundata-regex.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-regex.R:   2.
  > test-filter-immundata-regex.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-regex.R: i Checking if all files are of the same type
  > test-filter-immundata-regex.R: v All files have the same extension
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Renaming the columns and schemas 
  > test-filter-immundata-regex.R: v Renaming is finished
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Preprocessing the data 
  > test-filter-immundata-regex.R:   1. exclude_columns
  > test-filter-immundata-regex.R:   2. filter_nonproductive
  > test-filter-immundata-regex.R: v Preprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Aggregating the data to receptors 
  > test-filter-immundata-regex.R: i No locus information found
  > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Reading repertoire data 
  > test-filter-immundata-lev.R:   1.
  > test-filter-immundata-lev.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata-lev.R:   2.
  > test-filter-immundata-lev.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata-lev.R: i Checking if all files are of the same type
  > test-filter-immundata-lev.R: v All files have the same extension
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > test-filter-immundata-lev.R: v Renaming is finished
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Preprocessing the data 
  > test-filter-immundata-lev.R:   1. exclude_columns
  > test-filter-immundata-lev.R:   2. filter_nonproductive
  > test-filter-immundata-lev.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Aggregating the data to receptors 
  > test-filter-immundata-lev.R: i No locus information found
  > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-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/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533afd64cc/annotations.parquet]
  > 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/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7a1842f7/annotations.parquet]
  > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533afd64cc/metadata.json]
  > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533afd64cc]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533afd64cc']
  > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533afd64cc']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Summary 
  > test-filter-immundata-regex.R: i Time elapsed: 27.75 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
  > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7a1842f7/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7a1842f7]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7a1842f7']
  > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a7a1842f7']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 25.3 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
  Saving _problems/test-filter-immundata-lev-24.R
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Reading repertoire data 
  > test-filter-receptors.R:   1.
  > test-filter-receptors.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-receptors.R:   2.
  > test-filter-receptors.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-receptors.R: i Checking if all files are of the same type
  > test-filter-receptors.R: v All files have the same extension
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Renaming the columns and schemas 
  > test-filter-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:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata.R:   2.
  > test-filter-immundata.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata.R: i Checking if all files are of the same type
  > test-filter-receptors.R: v Renaming is finished
  > test-filter-receptors.R: 
  > test-filter-immundata.R: v All files have the same extension
  > 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: 
  > 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-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:   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.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-immundata.R: v Joining plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Postprocessing the data 
  > test-filter-immundata.R:   1. prefix_barcodes
  > test-filter-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-immundata.R: v Postprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-filter-receptors.R: v Postprocessing plan is ready
  > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533deb05aa/annotations.parquet]
  > 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/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a67eeaa19/annotations.parquet]
  > test-filter-receptors.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a67eeaa19/metadata.json]
  > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a67eeaa19]
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a67eeaa19']
  > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/file1e9f5a67eeaa19']
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Summary 
  > test-filter-receptors.R: i Time elapsed: 27.62 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
  > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533deb05aa/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533deb05aa]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533deb05aa']
  > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f533deb05aa']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 26.3 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
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Reading repertoire data 
  > test-filter-immundata.R:   1.
  > test-filter-immundata.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-filter-immundata.R:   2.
  > test-filter-immundata.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-filter-immundata.R: i Checking if all files are of the same type
  > test-filter-immundata.R: v All files have the same extension
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: v Renaming is finished
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Preprocessing the data 
  > test-filter-immundata.R:   1. exclude_columns
  > test-filter-immundata.R:   2. filter_nonproductive
  > test-filter-immundata.R: v Preprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Aggregating the data to receptors 
  > test-filter-immundata.R: i No locus information found
  > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires.R: Rows: 2 Columns: 4
  > test-io-repertoires.R: -- Column specification --------------------------------------------------------
  > test-io-repertoires.R: Delimiter: "\t"
  > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
  > test-io-repertoires.R: 
  > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-io-repertoires.R: v Metadata parsed successfully
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R:   2.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R:   2. filter_nonproductive
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Postprocessing the data 
  > test-filter-immundata.R:   1. prefix_barcodes
  > test-filter-immundata.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata.R: v Postprocessing plan is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f537f1cce8f/annotations.parquet]
  > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f537f1cce8f/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f537f1cce8f]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f537f1cce8f']
  > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp2prj4z/file1e9f537f1cce8f']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 23 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
  > test-io-repertoires.R: v Joining plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Postprocessing the data 
  > test-io-repertoires.R:   1. prefix_barcodes
  > test-io-repertoires.R: v Postprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH']
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 31.54 secs
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires.R: v Loaded ImmunData with [1902] chains
  > test-io-repertoires.R: Rows: 2 Columns: 4
  > test-io-repertoires.R: -- Column specification --------------------------------------------------------
  > test-io-repertoires.R: Delimiter: "\t"
  > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
  > test-io-repertoires.R: 
  > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
  > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
  > test-io-repertoires.R: v Metadata parsed successfully
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R:   2.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R:   2. filter_nonproductive
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-io-repertoires.R: v Joining plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Postprocessing the data 
  > test-io-repertoires.R:   1. prefix_barcodes
  > test-io-repertoires.R: v Postprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH']
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 38.67 secs
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires.R: v Loaded ImmunData with [1902] chains
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R:   2. filter_nonproductive
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Postprocessing the data 
  > test-io-repertoires.R:   1. prefix_barcodes
  > test-io-repertoires.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires.R: v Postprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-no-barcodes/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-no-barcodes/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-no-barcodes]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-no-barcodes']
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-no-barcodes']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 12.78 secs
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires.R: v Loaded ImmunData with [955] chains
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R:   2. filter_nonproductive
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Postprocessing the data 
  > test-io-repertoires.R:   1. prefix_barcodes
  > test-io-repertoires.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires.R: v Postprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude']
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 13.47 secs
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL]
  > test-io-repertoires.R: v Loaded ImmunData with [1000] chains
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Introduced new renamed columns: v_gene
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R:   2. filter_nonproductive
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Postprocessing the data 
  > test-io-repertoires.R:   1. prefix_barcodes
  > test-io-repertoires.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires.R: v Postprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-rename/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-rename/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-rename]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-rename']
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-rename']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 12.32 secs
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL]
  > test-io-repertoires.R: v Loaded ImmunData with [955] chains
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Introduced new renamed columns: j_gene
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  > test-io-repertoires.R: i No locus information found
  > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Postprocessing the data 
  > test-io-repertoires.R:   1. prefix_barcodes
  > test-io-repertoires.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-io-repertoires.R: v Postprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Saving the newly created ImmunData to disk 
  > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude-rename/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude-rename/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude-rename]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude-rename']
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpHjaD7o/working_dir/Rtmp6zj0cH/test-exclude-rename']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 11.34 secs
  > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL]
  > test-io-repertoires.R: v Loaded ImmunData with [1000] chains
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R: i Checking if all files are of the same type
  > test-io-repertoires.R: v All files have the same extension
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-io-repertoires.R: v Renaming is finished
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Preprocessing the data 
  > test-io-repertoires.R:   1. exclude_columns
  > test-io-repertoires.R:   2. filter_nonproductive
  > test-io-repertoires.R: v Preprocessing plan is ready
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Aggregating the data to receptors 
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-filter-immundata-lev.R:21:3'): Levenshtein fuzzy matching returns correct results ──
  Expected `arrange(collect(out$receptors))` to equal `arrange(gold)`.
  Differences:
    `attr(actual, 'row.names')`: NA -3  
  `attr(expected, 'row.names')`:  1  2 3
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [9s/44s] OK
* checking HTML version of manual ... [5s/18s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/immundata.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 13:18.07, 297.38 + 18.17