Running ‘testthat.R’ [51s/33s]
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 0.0.5
  > 
  > 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:   /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-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-barcodes.R: 
  > test-annotate-barcodes.R: -- Renaming the columns and schemas 
  > test-annotate-barcodes.R: v Renaming is finished
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Preprocessing the data 
  > test-annotate-barcodes.R:   1. exclude_columns
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Renaming the columns and schemas 
  > test-annotate-barcodes.R:   2. filter_nonproductive
  > test-annotate-receptors.R: v Renaming is finished
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Preprocessing the data 
  > test-annotate-receptors.R:   1. exclude_columns
  > test-annotate-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-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/Rtmpoif4Lq/file19736d2e7f1c81/annotations.parquet]
  > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Postprocessing the data 
  > test-annotate-receptors.R:   1. prefix_barcodes
  > test-annotate-receptors.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-annotate-receptors.R: v Postprocessing plan is ready
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk 
  > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/RtmpJDX0as/file1973565ea05a44/annotations.parquet]
  > test-annotate-barcodes.R: i Writing the metadata to [/tmp/Rtmpoif4Lq/file19736d2e7f1c81/metadata.json]
  > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmpoif4Lq/file19736d2e7f1c81]
  > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpoif4Lq/file19736d2e7f1c81']
  > 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/Rtmpoif4Lq/file19736d2e7f1c81']
  > test-annotate-barcodes.R: 
  > test-annotate-barcodes.R: -- Summary 
  > test-annotate-barcodes.R: i Time elapsed: 2.53 secs
  Saving _problems/test-annotate-barcodes-2.R
  > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpJDX0as/file1973565ea05a44/metadata.json]
  > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpJDX0as/file1973565ea05a44]
  > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/file1973565ea05a44']
  > 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/RtmpJDX0as/file1973565ea05a44']
  > test-annotate-receptors.R: 
  > test-annotate-receptors.R: -- Summary 
  > test-annotate-receptors.R: i Time elapsed: 2.64 secs
  > 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 
  Saving _problems/test-annotate-receptors-2.R
  > 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:   /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-barcodes.R:   2. filter_nonproductive
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Renaming the columns and schemas 
  > 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: v Renaming is finished
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Preprocessing the data 
  > test-filter-immundata-exact.R:   1. exclude_columns
  > test-filter-immundata-exact.R:   2. filter_nonproductive
  > test-filter-immundata-exact.R: v Preprocessing plan is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Aggregating the data to receptors 
  > test-filter-immundata-exact.R: i No locus information found
  > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-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/Rtmpoif4Lq/file19736d57f8d46f/annotations.parquet]
  > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Postprocessing the data 
  > test-filter-immundata-exact.R:   1. prefix_barcodes
  > test-filter-immundata-exact.R:   ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
  > test-filter-immundata-exact.R: v Postprocessing plan is ready
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk 
  > test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/RtmpJDX0as/file197356fc9121b/annotations.parquet]
  > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmpoif4Lq/file19736d57f8d46f/metadata.json]
  > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmpoif4Lq/file19736d57f8d46f]
  > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmpoif4Lq/file19736d57f8d46f']
  > 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/Rtmpoif4Lq/file19736d57f8d46f']
  > test-filter-barcodes.R: 
  > test-filter-barcodes.R: -- Summary 
  > test-filter-barcodes.R: i Time elapsed: 2.31 secs
  Saving _problems/test-filter-barcodes-4.R
  > 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-exact.R: i Writing the metadata to [/tmp/RtmpJDX0as/file197356fc9121b/metadata.json]
  > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpJDX0as/file197356fc9121b]
  > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/file197356fc9121b']
  > 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/RtmpJDX0as/file197356fc9121b']
  > test-filter-immundata-exact.R: 
  > test-filter-immundata-exact.R: -- Summary 
  > test-filter-immundata-exact.R: i Time elapsed: 2.38 secs
  > 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
  Saving _problems/test-filter-immundata-exact-2.R
  > test-filter-immundata-hamm.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-hamm.R: v Preprocessing plan is ready
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Renaming the columns and schemas 
  > 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-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/Rtmpoif4Lq/file19736d2475ff9a/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/RtmpJDX0as/file1973564fea845b/annotations.parquet]
  > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmpoif4Lq/file19736d2475ff9a/metadata.json]
  > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmpoif4Lq/file19736d2475ff9a]
  > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmpoif4Lq/file19736d2475ff9a']
  > 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/Rtmpoif4Lq/file19736d2475ff9a']
  > test-filter-immundata-hamm.R: 
  > test-filter-immundata-hamm.R: -- Summary 
  > test-filter-immundata-hamm.R: i Time elapsed: 2.42 secs
  Saving _problems/test-filter-immundata-hamm-3.R
  > 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-lev.R: i Writing the metadata to [/tmp/RtmpJDX0as/file1973564fea845b/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpJDX0as/file1973564fea845b]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/file1973564fea845b']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Renaming the columns and schemas 
  > 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/RtmpJDX0as/file1973564fea845b']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 2.47 secs
  > 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-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-regex.R:   2. filter_nonproductive
  > 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-regex.R: v Preprocessing plan is ready
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Aggregating the data to receptors 
  > test-filter-immundata-regex.R: i No locus information found
  > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata-lev.R: v 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/Rtmpoif4Lq/file19736d6b86b5ed/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/RtmpJDX0as/file19735666d6459c/annotations.parquet]
  > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmpoif4Lq/file19736d6b86b5ed/metadata.json]
  > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmpoif4Lq/file19736d6b86b5ed]
  > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmpoif4Lq/file19736d6b86b5ed']
  > 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/Rtmpoif4Lq/file19736d6b86b5ed']
  > test-filter-immundata-regex.R: 
  > test-filter-immundata-regex.R: -- Summary 
  > test-filter-immundata-regex.R: i Time elapsed: 2.28 secs
  Saving _problems/test-filter-immundata-regex-2.R
  > 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-lev.R: i Writing the metadata to [/tmp/RtmpJDX0as/file19735666d6459c/metadata.json]
  > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpJDX0as/file19735666d6459c]
  > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/file19735666d6459c']
  > 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/RtmpJDX0as/file19735666d6459c']
  > test-filter-immundata-lev.R: 
  > test-filter-immundata-lev.R: -- Summary 
  > test-filter-immundata-lev.R: i Time elapsed: 2.44 secs
  > 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
  Saving _problems/test-filter-immundata-lev-3.R
  Saving _problems/test-filter-immundata-lev-29.R
  > test-filter-immundata.R:   2. filter_nonproductive
  > 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-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: 
  > test-filter-receptors.R: -- Renaming the columns and schemas 
  > test-filter-receptors.R: v Renaming is finished
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Preprocessing the data 
  > test-filter-receptors.R:   1. exclude_columns
  > test-filter-receptors.R:   2. filter_nonproductive
  > test-filter-receptors.R: v Preprocessing plan is ready
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Aggregating the data to receptors 
  > test-filter-receptors.R: i No locus information found
  > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
  > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column 
  > test-filter-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/RtmpJDX0as/file19735678d271b1/annotations.parquet]
  > 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: i Writing the metadata to [/tmp/RtmpJDX0as/file19735678d271b1/metadata.json]
  > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmpJDX0as/file19735678d271b1]
  > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/file19735678d271b1']
  > 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/RtmpJDX0as/file19735678d271b1']
  > test-filter-receptors.R: 
  > test-filter-receptors.R: -- Summary 
  > test-filter-receptors.R: i Time elapsed: 2.42 secs
  Saving _problems/test-filter-receptors-3.R
  > 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/Rtmpoif4Lq/file19736d152ac1b6/annotations.parquet]
  > 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R:   2.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpoif4Lq/file19736d152ac1b6/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpoif4Lq/file19736d152ac1b6]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpoif4Lq/file19736d152ac1b6']
  > 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/Rtmpoif4Lq/file19736d152ac1b6']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Renaming the columns and schemas 
  > test-filter-immundata.R: i Time elapsed: 3.3 secs
  > 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-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-io-repertoires.R:   2. filter_nonproductive
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Renaming the columns and schemas 
  > 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 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: 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: 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/Rtmpoif4Lq/file19736d7ec3c6f8/annotations.parquet]
  > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmpoif4Lq/file19736d7ec3c6f8/metadata.json]
  > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmpoif4Lq/file19736d7ec3c6f8]
  > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmpoif4Lq/file19736d7ec3c6f8']
  > 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/Rtmpoif4Lq/file19736d7ec3c6f8']
  > test-filter-immundata.R: 
  > test-filter-immundata.R: -- Summary 
  > test-filter-immundata.R: i Time elapsed: 2.32 secs
  > 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
  Saving _problems/test-filter-immundata-2.R
  Saving _problems/test-filter-immundata-20.R
  > 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/RtmpJDX0as/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJDX0as/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJDX0as]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as']
  > 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/RtmpJDX0as']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 3.15 secs
  > 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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
  > test-io-repertoires.R:   2.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/RtmpJDX0as/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJDX0as/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJDX0as]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as']
  > 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/RtmpJDX0as']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 3.3 secs
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/RtmpJDX0as/test-no-barcodes/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJDX0as/test-no-barcodes/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJDX0as/test-no-barcodes]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/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/RtmpJDX0as/test-no-barcodes']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 1.28 secs
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/RtmpJDX0as/test-exclude/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJDX0as/test-exclude/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJDX0as/test-exclude]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/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/RtmpJDX0as/test-exclude']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 1.34 secs
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/RtmpJDX0as/test-rename/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJDX0as/test-rename/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJDX0as/test-rename]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/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/RtmpJDX0as/test-rename']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 1.28 secs
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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/RtmpJDX0as/test-exclude-rename/annotations.parquet]
  > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJDX0as/test-exclude-rename/metadata.json]
  > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJDX0as/test-exclude-rename]
  > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJDX0as/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/RtmpJDX0as/test-exclude-rename']
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Summary 
  > test-io-repertoires.R: i Time elapsed: 1.26 secs
  > test-io-repertoires.R: 
  > test-io-repertoires.R: -- Reading repertoire data 
  > test-io-repertoires.R:   1.
  > test-io-repertoires.R:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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 
  Saving _problems/test-io-repertoires-28.R
  Saving _problems/test-io-repertoires-56.R
  Saving _problems/test-io-repertoires-83.R
  Saving _problems/test-io-repertoires-120.R
  Saving _problems/test-io-repertoires-146.R
  Saving _problems/test-io-repertoires-176.R
  [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  ── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ──
  Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
  i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
  i See `vignette("prudence")` for other options.
  Caused by error in `quo_is_null()`:
  ! `quo` must be a quosure
  
  [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
  Error:
  ! Test failures.
  Execution halted