CRAN Package Check Results for Package immundata

Last updated on 2026-03-19 07:57:52 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.0.5	10.98	219.73	230.71	OK
r-devel-linux-x86_64-debian-gcc	0.0.6	8.17	381.03	389.20	ERROR
r-devel-linux-x86_64-fedora-clang	0.0.6	24.00	1057.69	1081.69	OK
r-devel-linux-x86_64-fedora-gcc	0.0.6	20.00	873.72	893.72	OK
r-devel-macos-arm64	0.0.6	3.00	121.00	124.00	OK
r-devel-windows-x86_64	0.0.6	18.00	348.00	366.00	OK
r-patched-linux-x86_64	0.0.6	10.80	538.58	549.38	ERROR
r-release-linux-x86_64	0.0.5	10.13	169.05	179.18	OK
r-release-macos-arm64	0.0.5				OK
r-release-macos-x86_64	0.0.5	8.00	191.00	199.00	OK
r-release-windows-x86_64	0.0.6	9.00	348.00	357.00	OK
r-oldrel-macos-arm64	0.0.6				NOTE
r-oldrel-macos-x86_64	0.0.6	9.00	556.00	565.00	NOTE
r-oldrel-windows-x86_64	0.0.6	21.00	415.00	436.00	NOTE

Additional issues

MKL

Check Details

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [312s/161s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > 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-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: 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/RtmpG3O9vQ/file59fca5cdcd468/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-barcodes.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca5cdcd468/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca5cdcd468] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca5cdcd468'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca5cdcd468'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 3.73 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb17e688639/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb17e688639/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb17e688639] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb17e688639'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb17e688639'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.3 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb16260f0a9/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb16260f0a9/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb16260f0a9] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb16260f0a9'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb16260f0a9'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.11 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca3061bdd6/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca3061bdd6/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca3061bdd6] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3061bdd6'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3061bdd6'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.5 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb13b0cb8ad/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb13b0cb8ad/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb13b0cb8ad] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb13b0cb8ad'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb13b0cb8ad'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.07 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca3cd8c112/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca3cd8c112/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca3cd8c112] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3cd8c112'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3cd8c112'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.14 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb120ed6aa4/annotations.parquet] > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca6cb598a7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb120ed6aa4/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb120ed6aa4] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb120ed6aa4'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb120ed6aa4'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.11 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca6cb598a7/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca6cb598a7] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca6cb598a7'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca6cb598a7'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.07 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca14eba094/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca14eba094/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca14eba094] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca14eba094'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca14eba094'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.13 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb162155ecf/annotations.parquet] > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb162155ecf/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb162155ecf] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb162155ecf'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb162155ecf'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.1 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca3de9cd5a/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca3de9cd5a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca3de9cd5a] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3de9cd5a'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3de9cd5a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.21 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb131f723cb/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb131f723cb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb131f723cb] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb131f723cb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb131f723cb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.99 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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/RtmpG3O9vQ/file59fca3e77503d/annotations.parquet] > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca3e77503d/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca3e77503d] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3e77503d'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca3e77503d'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 3.21 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: 2. filter_nonproductive > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb1176a1dc3/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb1176a1dc3/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb1176a1dc3] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1176a1dc3'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1176a1dc3'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.23 secs > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca1a4901a7/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca1a4901a7/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca1a4901a7] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca1a4901a7'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca1a4901a7'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.11 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb1773e4eeb/annotations.parquet] > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fcaeea0d4a/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb1773e4eeb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb1773e4eeb] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1773e4eeb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1773e4eeb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.85 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fcaeea0d4a/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fcaeea0d4a] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fcaeea0d4a'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fcaeea0d4a'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.65 secs > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb118f069c6/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb118f069c6/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb118f069c6] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb118f069c6'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb118f069c6'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 3.56 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca4de8efbe/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca4de8efbe/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca4de8efbe] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca4de8efbe'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca4de8efbe'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.6 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb1435eeed0/annotations.parquet] > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb1435eeed0/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb1435eeed0] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1435eeed0'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1435eeed0'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.1 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca175f01b5/annotations.parquet] > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca175f01b5/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca175f01b5] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca175f01b5'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca175f01b5'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.32 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca2c1728a5/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb160c54deb/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca2c1728a5/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca2c1728a5] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca2c1728a5'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca2c1728a5'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 3.13 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb160c54deb/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb160c54deb] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb160c54deb'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb160c54deb'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.15 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-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/RtmpG3O9vQ/file59fca934160/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca934160/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca934160] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca934160'] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca934160'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-exact.R: i Time elapsed: 3.37 secs > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. > test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-hamm.R: i Checking if all files are of the same type > test-filter-immundata-hamm.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb1494c3707/annotations.parquet] > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb1494c3707/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb1494c3707] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1494c3707'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb1494c3707'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.21 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca1e20ca38/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca1e20ca38/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca1e20ca38] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca1e20ca38'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca1e20ca38'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.39 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb17a05e859/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb17a05e859/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb17a05e859] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb17a05e859'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb17a05e859'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.1 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-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/RtmpG3O9vQ/file59fca313f235c/annotations.parquet] > 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: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca313f235c/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca313f235c] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca313f235c'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca313f235c'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.23 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-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/RtmpSGh7I4/file59fb144b84366/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb144b84366/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb144b84366] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb144b84366'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb144b84366'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 3.21 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > 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/RtmpG3O9vQ/file59fca70a0c33f/annotations.parquet] > 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-lev.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca70a0c33f/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca70a0c33f] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca70a0c33f'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca70a0c33f'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.29 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/file59fb128a1c4b4/annotations.parquet] > 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/RtmpG3O9vQ/file59fcaa58978e/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb128a1c4b4/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb128a1c4b4] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb128a1c4b4'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb128a1c4b4'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.02 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-receptors.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fcaa58978e/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fcaa58978e] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fcaa58978e'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fcaa58978e'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 3.29 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: 2. filter_nonproductive > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: 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-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/legacy_v1_59fca125ed66/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/legacy_v1_59fca125ed66/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/legacy_v1_59fca125ed66] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/legacy_v1_59fca125ed66'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/legacy_v1_59fca125ed66'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.45 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/legacy_v1_59fca125ed66'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: 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/RtmpSGh7I4/file59fb11620cdda/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpSGh7I4/file59fb11620cdda/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/file59fb11620cdda] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb11620cdda'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/file59fb11620cdda'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.06 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg-stepwise.R: 1. /tmp/RtmpSGh7I4/file59fb15a1ac36f.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb14919478/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb14919478/metadata.json] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb14919478] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb14919478'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.52 secs > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb14919478'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpSGh7I4/file59fb14804548e.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb150b64885/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb150b64885/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb150b64885] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb150b64885'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb150b64885'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.3 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.52 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpSGh7I4/file59fb17055bf3f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb122b21ab6/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb122b21ab6/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb122b21ab6] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb122b21ab6'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb122b21ab6'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.03 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.51 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpSGh7I4/file59fb125b50394.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb11d862e5d/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb11d862e5d/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb11d862e5d] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb11d862e5d'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb11d862e5d'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpSGh7I4/file59fb14ab7911f.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb15c21f5a8/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb15c21f5a8/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb15c21f5a8] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb15c21f5a8'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb15c21f5a8'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.97 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpSGh7I4/file59fb14745ed86.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb1551fa85e/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb1551fa85e/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb1551fa85e] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1551fa85e'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1551fa85e'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.96 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.57 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpSGh7I4/file59fb143acf979.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb16542b832/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb16542b832/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb16542b832] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb16542b832'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb16542b832'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.07 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.47 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb122f6135e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb154bc05fb/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb154bc05fb/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb154bc05fb] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb154bc05fb'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb154bc05fb'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.26 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb169447e57.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb11de5f1db/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb11de5f1db/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb11de5f1db] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb11de5f1db'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb11de5f1db'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.27 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb1218cc1c7.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb17d1dbc8e/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.52 secs > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb17d1dbc8e/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb17d1dbc8e] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb17d1dbc8e'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb17d1dbc8e'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-counts.R: i Time elapsed: 0.94 secs > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb156d2781d.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectB'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb14c5a9382/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb14c5a9382/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb14c5a9382] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb14c5a9382'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb14c5a9382'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.97 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb14cf69a79.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb130b4f060/annotations.parquet] > test-io-immundata.R: i Time elapsed: 1.54 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb130b4f060/metadata.json] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb130b4f060] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb130b4f060'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb130b4f060'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.98 secs > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb163537f2c.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb1f2a9130/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb1f2a9130/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb1f2a9130] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1f2a9130'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1f2a9130'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.12 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb168715ea7.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb12d43cf0d/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb12d43cf0d/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb12d43cf0d] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb12d43cf0d'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb12d43cf0d'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.16 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb127e7dd9.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Time elapsed: 1.49 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb1486e0444/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb1486e0444/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb1486e0444] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1486e0444'] > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1486e0444'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.95 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpSGh7I4/file59fb127e7dd9.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb13c9087ff/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb13c9087ff/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb13c9087ff] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb13c9087ff'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb13c9087ff'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.08 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca641d5386/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb134e4029c/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca641d5386/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca641d5386] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca641d5386'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca641d5386'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.28 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb134e4029c/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb134e4029c] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb134e4029c'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb134e4029c'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.51 secs > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-immundata.R: v Renaming is finished > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.53 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb146d6a6f5/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb146d6a6f5/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb146d6a6f5] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb146d6a6f5'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb146d6a6f5'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.68 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.59 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb111197b87/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb111197b87/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb111197b87] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb111197b87'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb111197b87'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.65 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca49f0c431/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca49f0c431/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca49f0c431] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca49f0c431'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca49f0c431'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.34 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb1471e74df/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb1471e74df/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb1471e74df] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1471e74df'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb1471e74df'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.39 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/file59fca73fdb77d/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/file59fca73fdb77d/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/file59fca73fdb77d] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca73fdb77d'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/file59fca73fdb77d'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.43 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test-exclude/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb13291c5b5/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.63 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb13291c5b5/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb13291c5b5] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb13291c5b5'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb13291c5b5'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.44 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.81 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test-exclude-rename/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb141c72784/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.7 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb141c72784/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb141c72784] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb141c72784'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb141c72784'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.46 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test_immundata_59fca3ddd8b1e/annotations.parquet] > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb186e57be/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test_immundata_59fca3ddd8b1e/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test_immundata_59fca3ddd8b1e] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca3ddd8b1e'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca3ddd8b1e'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 17.69 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb186e57be/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb186e57be] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb186e57be'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb186e57be'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 22.14 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test_immundata_59fca39d1de1c/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test_immundata_59fca39d1de1c/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test_immundata_59fca39d1de1c] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca39d1de1c'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca39d1de1c'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 3.89 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/RtmpG3O9vQ/file59fcaefc3167.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test_immundata_59fca16c7992e/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test_immundata_59fca16c7992e/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test_immundata_59fca16c7992e] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca16c7992e'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca16c7992e'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.31 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /tmp/RtmpG3O9vQ/file59fca4cd8292e.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test_immundata_59fca74d000da/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test_immundata_59fca74d000da/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test_immundata_59fca74d000da] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca74d000da'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test_immundata_59fca74d000da'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.28 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/tmp/RtmpG3O9vQ/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/RtmpG3O9vQ/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/RtmpG3O9vQ/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmpG3O9vQ/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 1.79 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb11c73b271/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb11c73b271/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb11c73b271] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb11c73b271'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb11c73b271'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 23.36 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmpSGh7I4/file59fb1605dbf9.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb130f2e459/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb130f2e459/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb130f2e459] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb130f2e459'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb130f2e459'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.15 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /tmp/RtmpSGh7I4/file59fb169f6d4fe.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/tmp/RtmpSGh7I4/test_immundata_59fb144c5577a/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpSGh7I4/test_immundata_59fb144c5577a/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpSGh7I4/test_immundata_59fb144c5577a] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb144c5577a'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpSGh7I4/test_immundata_59fb144c5577a'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.01 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [454s/239s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.6 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: 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 [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244ff50c65/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244ff50c65/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244ff50c65] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244ff50c65'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244ff50c65'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 6.47 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5a9bbc3e/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5a9bbc3e/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5a9bbc3e] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5a9bbc3e'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5a9bbc3e'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 7.43 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a36b40e09/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a36b40e09/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a36b40e09] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a36b40e09'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a36b40e09'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624436e24f6c/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624436e24f6c/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624436e24f6c] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file12624436e24f6c'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file12624436e24f6c'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 5.05 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5e413bae/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5e413bae/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5e413bae] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5e413bae'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a5e413bae'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.26 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244529cfdb4/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244529cfdb4/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244529cfdb4] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244529cfdb4'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244529cfdb4'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.73 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d405365/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3acdb0ee/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d405365/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d405365] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d405365'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d405365'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.71 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3acdb0ee/metadata.json] > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3acdb0ee] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3acdb0ee'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3acdb0ee'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.13 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443813d859/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443813d859/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443813d859] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443813d859'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443813d859'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.72 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6aa896bc/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6aa896bc/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6aa896bc] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6aa896bc'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6aa896bc'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.11 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244a1e3e6f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244a1e3e6f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244a1e3e6f] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244a1e3e6f'] > test-annotate-external.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244a1e3e6f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 4.72 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a76dd38c9/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a76dd38c9/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a76dd38c9] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a76dd38c9'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a76dd38c9'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.38 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244d095207/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244d095207/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244d095207] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244d095207'] > test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244d095207'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 5.07 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262442f75bac4/annotations.parquet] > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3fa61043/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262442f75bac4/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262442f75bac4] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262442f75bac4'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262442f75bac4'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.06 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3fa61043/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3fa61043] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3fa61043'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a3fa61043'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.68 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443c17ca5a/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443c17ca5a/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443c17ca5a] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443c17ca5a'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262443c17ca5a'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.18 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Respons > test-compute-collect-immundata.R: e, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a4ebb46c7/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a4ebb46c7/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a4ebb46c7] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a4ebb46c7'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a4ebb46c7'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 5.99 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d88c0da/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d88c0da/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d88c0da] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d88c0da'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444d88c0da'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.09 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6484248/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6484248/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6484248] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6484248'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6484248'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.14 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Joining plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Postprocessing the data > test-compute-collect-immundata.R: 1. prefix_barcodes > test-compute-collect-immundata.R: v Postprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Saving the newly created ImmunData to disk > test-compute-collect-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262447a7e60d7/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262447a7e60d7/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262447a7e60d7] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262447a7e60d7'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262447a7e60d7'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 6.69 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a72bb8880/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a72bb8880/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a72bb8880] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a72bb8880'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a72bb8880'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.12 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-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 [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244162c36d7/annotations.parquet] > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244162c36d7/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244162c36d7] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244162c36d7'] > test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244162c36d7'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 4.81 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6be29bf8/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 [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624431a0664/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6be29bf8/metadata.json] > test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624431a0664/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6be29bf8] > test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624431a0664] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6be29bf8'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file12624431a0664'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file12624431a0664'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a6be29bf8'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.38 secs > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 4.82 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains and [1668] receptors > 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-patched-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-patched-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-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-agg-strata.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244685478a6/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244685478a6/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244685478a6] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244685478a6'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244685478a6'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 4.75 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: > 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-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a41786987/annotations.parquet] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a41786987/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a41786987] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a41786987'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a41786987'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-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 [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444e2e2da9/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444e2e2da9/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444e2e2da9] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444e2e2da9'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262444e2e2da9'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.99 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a48425544/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a48425544/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a48425544] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a48425544'] > test-agg-strata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a48425544'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 6.7 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-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-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: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262445c2d88a7/annotations.parquet] > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262445c2d88a7/metadata.json] > 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 ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file1262445c2d88a7] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262445c2d88a7'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file1262445c2d88a7'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 4.92 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37d3df56/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37d3df56/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37d3df56] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37d3df56'] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37d3df56'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 4.75 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 and [1668] receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-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-patched-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 Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: > test-filter-receptors.R: -- 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 Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244eb7092b/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244eb7092b/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file126244eb7092b] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244eb7092b'] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file126244eb7092b'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 6.18 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a9510dcf/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a9510dcf/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a9510dcf] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a9510dcf'] > test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a9510dcf'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 4.66 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: 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 [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624472e4a457/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/legacy_v1_12624a4e435081/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624472e4a457/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/file12624472e4a457] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/legacy_v1_12624a4e435081/metadata.json] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file12624472e4a457'] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/legacy_v1_12624a4e435081] > test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/file12624472e4a457'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/legacy_v1_12624a4e435081'] > test-filter-immundata.R: i Time elapsed: 4.75 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/legacy_v1_12624a4e435081'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.29 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/legacy_v1_12624a4e435081'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file126244daace48.tsv > test-io-repertoires-agg-stepwise.R: i Checking if all files are of the same type > test-io-repertoires-agg-stepwise.R: v All files have the same extension > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Aggregating the data to receptors > test-io-repertoires-agg-stepwise.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg-stepwise.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg-stepwise.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg-stepwise.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262444bf3a641/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262444bf3a641/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262444bf3a641] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262444bf3a641'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262444bf3a641'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.36 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624419506bb5.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624439d5b270/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624439d5b270/metadata.json] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624439d5b270] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624439d5b270'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624439d5b270'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.42 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.17 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262446551977b.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441e8f0626/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441e8f0626/metadata.json] > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441e8f0626] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441e8f0626'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441e8f0626'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.56 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [3] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.19 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262447b646d35.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244332c35e4/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244332c35e4/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244332c35e4] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244332c35e4'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244332c35e4'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.61 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624423faaae7.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.43 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: Rows: 2 Columns: 4 > test-io-immundata.R: -- Column specification -------------------------------------------------------- > test-io-immundata.R: Delimiter: "\t" > test-io-immundata.R: chr (4): File, Therapy, Response, Prefix > test-io-immundata.R: > test-io-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-immundata.R: v Metadata parsed successfully > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624467677f74/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624467677f74/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624467677f74] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624467677f74'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624467677f74'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.56 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624429421156.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447033244/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447033244/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447033244] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447033244'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447033244'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.6 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624419b96ef3.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Preprocessing the data > test-io-repertoires-agg.R: 1. exclude_columns > test-io-repertoires-agg.R: 2. filter_nonproductive > test-io-repertoires-agg.R: ! No columns with the productive specification found; skipping the filtering > test-io-repertoires-agg.R: v Preprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Joining plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Postprocessing the data > test-io-repertoires-agg.R: 1. prefix_barcodes > test-io-repertoires-agg.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-agg.R: v Postprocessing plan is ready > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451fbf29f/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 5.3 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451fbf29f/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451fbf29f] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451fbf29f'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451fbf29f'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 1.96 secs > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-agg.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262444470141e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442507e79a/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442507e79a/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442507e79a] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442507e79a'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442507e79a'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.42 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262444df36fa3.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624420627f0/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624420627f0/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624420627f0] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624420627f0'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624420627f0'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.47 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [3] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262445fa1352e.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.24 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624423c5c91c/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624423c5c91c/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624423c5c91c] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624423c5c91c'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624423c5c91c'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.6 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262447d0e4a4c.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447dd99d87/annotations.parquet] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.25 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447dd99d87/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447dd99d87] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447dd99d87'] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262447dd99d87'] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/annotations.parquet] > test-io-repertoires-counts.R: i Time elapsed: 1.59 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB'] > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624476a2183b.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451cfa545/annotations.parquet > test-io-repertoires-counts.R: ] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451cfa545/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451cfa545] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451cfa545'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624451cfa545'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.59 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624426f32775.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.24 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624447f9df38/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624447f9df38/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624447f9df38] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624447f9df38'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624447f9df38'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.93 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file126244524292df.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-counts.R: i Processing data as bulk sequencing immune repertoires - with counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624448bfbe7f/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624448bfbe7f/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624448bfbe7f] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624448bfbe7f'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624448bfbe7f'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.26 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262447db37949.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.22 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446d20d78/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446d20d78/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446d20d78] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446d20d78'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446d20d78'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.51 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262447db37949.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-counts.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-counts.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624421d3ac18/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624421d3ac18/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624421d3ac18] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624421d3ac18'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624421d3ac18'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.77 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL|IGK")] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [2] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1af532c/annotations.parquet] > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624425a39dbb/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624425a39dbb/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624425a39dbb] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624425a39dbb'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624425a39dbb'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.33 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1af532c/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1af532c] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1af532c'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1af532c'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.89 secs > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.22 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectB/snapshots/baseline/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441ee1af33/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441ee1af33/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441ee1af33] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441ee1af33'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262441ee1af33'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.31 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 2.22 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/imd_snap_tests/projectA/snapshots/ops/v001'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442042d471/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442042d471/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442042d471] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442042d471'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262442042d471'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 4.4 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1a8166b1/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1a8166b1/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1a8166b1] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1a8166b1'] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a1a8166b1'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.75 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: 2. > test-io-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Preprocessing the data > test-io-immundata.R: 1. exclude_columns > test-io-immundata.R: 2. filter_nonproductive > test-io-immundata.R: v Preprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624419659533/annotations.parquet] > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Postprocessing the data > test-io-immundata.R: 1. prefix_barcodes > test-io-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-immundata.R: v Postprocessing plan is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37712b2e/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624419659533/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624419659533] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624419659533'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624419659533'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.58 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: Rows: 2 Columns: 4 > test-io-repertoires-files.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-files.R: Delimiter: "\t" > test-io-repertoires-files.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-files.R: > test-io-repertoires-files.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-files.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-files.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-files.R: v Metadata parsed successfully > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37712b2e/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37712b2e] > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37712b2e'] > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/file12624a37712b2e'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 4.82 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.31 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Introduced new renamed columns: v_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244261e10d3/annotations.parquet] > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test-rename/metadata.json] > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244261e10d3/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244261e10d3] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244261e10d3'] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.59 secs > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244261e10d3'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.23 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-processing.R: v Introduced new renamed columns: j_gene > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 2.49 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-files.R: v Joining plan is ready > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-files.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445d982d5b/annotations.parquet] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-files.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445d982d5b/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445d982d5b] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445d982d5b'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445d982d5b'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 5.43 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: Rows: 2 Columns: 4 > test-io-repertoires-processing.R: -- Column specification -------------------------------------------------------- > test-io-repertoires-processing.R: Delimiter: "\t" > test-io-repertoires-processing.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires-processing.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires-processing.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires-processing.R: v Metadata parsed successfully > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: 2. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating the data to receptors > test-io-repertoires-processing.R: i No locus information found > test-io-repertoires-processing.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires-processing.R: v Joining plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Aggregating repertoires... > test-io-repertoires-processing.R: v Aggregation is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a61f787de/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a61f787de/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a61f787de] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a61f787de'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a61f787de'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 25.6 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with the repertoire schema: [Therapy] > test-io-repertoires-processing.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624412e40a80/annotations.parquet] Saving _problems/test-io-repertoires-processing-90.R Saving _problems/test-io-repertoires-processing-110.R > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. > test-io-repertoires-schema-single.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624412e40a80/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624412e40a80] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624412e40a80'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_12624412e40a80'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 31.61 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [944] chains and [470] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found relaxed locus pair: IGH + (IGK|IGL). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a6bb66acf/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a6bb66acf/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a6bb66acf] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a6bb66acf'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a6bb66acf'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 5.35 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [915] chains and [907] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmprJaKs7/file12624a24e38583.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a3ade4c5d/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a3ade4c5d/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a3ade4c5d] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a3ade4c5d'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a3ade4c5d'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.39 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Reading repertoire data > test-io-repertoires-schema-single.R: 1. /home/hornik/tmp/scratch/RtmprJaKs7/file12624a716a9e9f.tsv > test-io-repertoires-schema-single.R: i Checking if all files are of the same type > test-io-repertoires-schema-single.R: v All files have the same extension > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Aggregating the data to receptors > test-io-repertoires-schema-single.R: i Found target locus: IGH. The dataset will be pre-filtered to leave chains for this locus only > test-io-repertoires-schema-single.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-single.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-single.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a49925e9d/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a49925e9d/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a49925e9d] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a49925e9d'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test_immundata_12624a49925e9d'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.42 secs > test-io-repertoires-schema-single.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-schema-single.R: v Loaded ImmunData with [1] chains and [1] receptors > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Reading repertoire data > test-io-repertoires-schema-table.R: 1. > test-io-repertoires-schema-table.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema-table.R: i Checking if all files are of the same type > test-io-repertoires-schema-table.R: v All files have the same extension > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Renaming the columns and schemas > test-io-repertoires-schema-table.R: v Renaming is finished > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Preprocessing the data > test-io-repertoires-schema-table.R: 1. exclude_columns > test-io-repertoires-schema-table.R: 2. filter_nonproductive > test-io-repertoires-schema-table.R: v Preprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Aggregating the data to receptors > test-io-repertoires-schema-table.R: i No locus information found > test-io-repertoires-schema-table.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-schema-table.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Postprocessing the data > test-io-repertoires-schema-table.R: 1. prefix_barcodes > test-io-repertoires-schema-table.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-schema-table.R: v Postprocessing plan is ready > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-table.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmprJaKs7/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmprJaKs7/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmprJaKs7/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmprJaKs7/test-no-barcodes'] > test-io-repertoires-schema-table.R: > test-io-repertoires-schema-table.R: -- Summary > test-io-repertoires-schema-table.R: i Time elapsed: 2.66 secs > test-io-repertoires-schema-table.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-schema-table.R: v Loaded ImmunData with [955] chains and [871] receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Reading repertoire data > test-io-repertoires-schema.R: 1. > test-io-repertoires-schema.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-schema.R: i Checking if all files are of the same type > test-io-repertoires-schema.R: v All files have the same extension > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Renaming the columns and schemas > test-io-repertoires-schema.R: v Renaming is finished > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Preprocessing the data > test-io-repertoires-schema.R: 1. exclude_columns > test-io-repertoires-schema.R: 2. filter_nonproductive > test-io-repertoires-schema.R: v Preprocessing plan is ready > test-io-repertoires-schema.R: > test-io-repertoires-schema.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445a064d73/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445a064d73/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445a064d73] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445a064d73'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262445a064d73'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 33.22 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGK|IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [1814] chains and [901] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file1262441eff2ac6.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446773287b/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446773287b/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446773287b] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446773287b'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_1262446773287b'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.6 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. /home/hornik/tmp/scratch/RtmpkpTFJX/file12624422454245.tsv > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-schema-paired.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-schema-paired.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244ec9b967/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244ec9b967/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244ec9b967] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244ec9b967'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpkpTFJX/test_immundata_126244ec9b967'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.58 secs > test-io-repertoires-schema-paired.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-schema-paired.R: v Loaded ImmunData with [2] chains and [1] receptors [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-io-repertoires-processing.R:87:3'): read_repertoires() removes non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:87:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires-processing.R:106:3'): read_repertoires() correctly reads non-productive ── Error in `compute_parquet(idata$annotations, annotations_path, options = parquet_options)`: {"exception_type":"IO","exception_message":"Failed to write '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet': Cannot open file \"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/tmp_annotations.parquet\": Read-only file system","errno":"30"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires-processing.R:106:3 2. │ └─immundata:::write_immundata_internal(...) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(idata$annotations, annotations_path, options = parquet_options) 5. │ └─duckdb$rel_to_parquet(rel, path, options) 6. │ └─duckdb:::rethrow_rapi_rel_to_parquet(rel, file_name, options) 7. │ ├─rlang::try_fetch(...) 8. │ │ ├─base::tryCatch(...) 9. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. │ │ └─base::withCallingHandlers(...) 13. │ └─duckdb:::rapi_rel_to_parquet(rel, file_name, options_sexps) 14. └─base::.handleSimpleError(...) 15. └─rlang (local) h(simpleError(msg, call)) 16. └─handlers[[1L]](cnd) 17. └─duckdb:::rethrow_error_from_rapi(e, call) 18. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 349 ] Error: ! Test failures. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.0.6
Check: Rd cross-references
Result: NOTE Unknown package ‘anndataR’ in Rd xrefs Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

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