CRAN Package Check Results for Maintainer ‘Vadim I. Nazarov <support at immunomind.com>’

Last updated on 2026-03-18 00:50:41 CET.

Package	ERROR	NOTE	OK
immunarch	2	2	10
immundata	3	1	10

Package immunarch

Current CRAN status: ERROR: 2, NOTE: 2, OK: 10

Version: 0.10.3
Check: examples
Result: ERROR Running examples in 'immunarch-Ex.R' failed The error most likely occurred in: > ### Name: airr_public > ### Title: Public indices - pairwise repertoire overlap > ### Aliases: airr_public airr_public_intersection airr_public_jaccard > > ### ** Examples > > # Limit the number of threads used by the underlying DB for this session. > # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers). > db_exec("SET threads TO 1") > # Load data > immdata <- get_test_idata() |> agg_repertoires("Therapy") Rows: 2 Columns: 4 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (4): File, Therapy, Response, Prefix ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. ℹ Found 2/2 repertoire files from the metadata on the disk ✔ Metadata parsed successfully ── Reading repertoire data 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv ℹ Checking if all files are of the same type ✔ All files have the same extension ── Renaming the columns and schemas ✔ Renaming is finished ── Preprocessing the data 1. exclude_columns 2. filter_nonproductive ✔ Preprocessing plan is ready ── Aggregating the data to receptors ℹ No locus information found ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible ✔ Execution plan for receptor data aggregation and annotation is ready ── Joining the metadata table with the dataset using 'filename' column ✔ Joining plan is ready ── Postprocessing the data 1. prefix_barcodes ✔ Postprocessing plan is ready ── Saving the newly created ImmunData to disk ℹ Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\RtmpUdTkC4\file2e0c738a1fc8/annotations.parquet] Error in `duckfun()`: ! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy") 2. │ └─checkmate::assert_r6(idata, "ImmunData") 3. │ └─checkmate::checkR6(...) 4. ├─immundata::get_test_idata() 5. │ └─immundata:::get_test_idata_tsv_with_metadata() 6. │ └─immundata::read_repertoires(...) 7. │ └─immundata::write_immundata(idata, output_folder) 8. │ ├─duckplyr::compute_parquet(...) 9. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 11. │ └─duckplyr::read_file_duckdb(...) 12. │ └─duckplyr:::duckfun(...) 13. │ └─duckdb$rel_from_table_function(...) 14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 15. │ ├─rlang::try_fetch(...) 16. │ │ ├─base::tryCatch(...) 17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ │ └─base::withCallingHandlers(...) 21. │ └─duckdb:::rapi_rel_from_table_function(...) 22. └─base::.handleSimpleError(...) 23. └─rlang (local) h(simpleError(msg, call)) 24. └─handlers[[1L]](cnd) 25. └─duckdb:::rethrow_error_from_rapi(e, call) 26. └─rlang::abort(msg, call = call) Execution halted Flavor: r-devel-windows-x86_64

Version: 0.10.3
Check: examples
Result: ERROR Running examples in 'immunarch-Ex.R' failed The error most likely occurred in: > ### Name: airr_public > ### Title: Public indices - pairwise repertoire overlap > ### Aliases: airr_public airr_public_intersection airr_public_jaccard > > ### ** Examples > > # Limit the number of threads used by the underlying DB for this session. > # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers). > db_exec("SET threads TO 1") > # Load data > immdata <- get_test_idata() |> agg_repertoires("Therapy") Rows: 2 Columns: 4 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (4): File, Therapy, Response, Prefix ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. ℹ Found 2/2 repertoire files from the metadata on the disk ✔ Metadata parsed successfully ── Reading repertoire data 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv ℹ Checking if all files are of the same type ✔ All files have the same extension ── Renaming the columns and schemas ✔ Renaming is finished ── Preprocessing the data 1. exclude_columns 2. filter_nonproductive ✔ Preprocessing plan is ready ── Aggregating the data to receptors ℹ No locus information found ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible ✔ Execution plan for receptor data aggregation and annotation is ready ── Joining the metadata table with the dataset using 'filename' column ✔ Joining plan is ready ── Postprocessing the data 1. prefix_barcodes ✔ Postprocessing plan is ready ── Saving the newly created ImmunData to disk ℹ Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\RtmpKMUbZQ\file37f862ff5a2f/annotations.parquet] Error in `duckfun()`: ! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy") 2. │ └─checkmate::assert_r6(idata, "ImmunData") 3. │ └─checkmate::checkR6(...) 4. ├─immundata::get_test_idata() 5. │ └─immundata:::get_test_idata_tsv_with_metadata() 6. │ └─immundata::read_repertoires(...) 7. │ └─immundata::write_immundata(idata, output_folder) 8. │ ├─duckplyr::compute_parquet(...) 9. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 11. │ └─duckplyr::read_file_duckdb(...) 12. │ └─duckplyr:::duckfun(...) 13. │ └─duckdb$rel_from_table_function(...) 14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 15. │ ├─rlang::try_fetch(...) 16. │ │ ├─base::tryCatch(...) 17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 20. │ │ └─base::withCallingHandlers(...) 21. │ └─duckdb:::rapi_rel_from_table_function(...) 22. └─base::.handleSimpleError(...) 23. └─rlang (local) h(simpleError(msg, call)) 24. └─handlers[[1L]](cnd) 25. └─duckdb:::rethrow_error_from_rapi(e, call) 26. └─rlang::abort(msg, call = call) Execution halted Flavor: r-release-windows-x86_64

Version: 0.10.3
Check: installed package size
Result: NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 2.4Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package immundata

Current CRAN status: ERROR: 3, NOTE: 1, OK: 10

Additional issues

MKL

Version: 0.0.6
Check: tests
Result: ERROR Running ‘testthat.R’ [309s/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-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > 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: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d76d10a30c/annotations.parquet] > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-barcodes.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d76d10a30c/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d76d10a30c] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d76d10a30c'] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d76d10a30c'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 3.55 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/file3968a85e8130cc/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a85e8130cc/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a85e8130cc] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a85e8130cc'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a85e8130cc'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.38 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-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-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: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/file3968a82ff6fc54/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a82ff6fc54/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a82ff6fc54] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a82ff6fc54'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a82ff6fc54'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.06 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d74aa5972c/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d74aa5972c/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d74aa5972c] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d74aa5972c'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d74aa5972c'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.41 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/file3968a863cf587/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a863cf587/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a863cf587] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a863cf587'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a863cf587'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.22 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d76682b7df/annotations.parquet] > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d76682b7df/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d76682b7df] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d76682b7df'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d76682b7df'] > 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-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d72a7b4d3d/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/RtmplIpVT4/file3968a839155fc2/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d72a7b4d3d/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d72a7b4d3d] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d72a7b4d3d'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d72a7b4d3d'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.12 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a839155fc2/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a839155fc2] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a839155fc2'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a839155fc2'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > 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: i Time elapsed: 4.04 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-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-external.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-external.R: > test-annotate-external.R: -- Postprocessing the data > test-annotate-external.R: 1. prefix_barcodes > test-annotate-external.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-external.R: v Postprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Saving the newly created ImmunData to disk > test-annotate-external.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d718ff974a/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/RtmpnmmaPx/file3968d718ff974a/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d718ff974a] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d718ff974a'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d718ff974a'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.29 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-external.R: > test-annotate-external.R: -- Reading repertoire data > test-annotate-external.R: 1. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-external.R: 2. > test-annotate-external.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-external.R: i Checking if all files are of the same type > test-annotate-external.R: v All files have the same extension > test-annotate-external.R: > test-annotate-external.R: -- Renaming the columns and schemas > test-annotate-external.R: v Renaming is finished > test-annotate-external.R: > test-annotate-external.R: -- Preprocessing the data > test-annotate-external.R: 1. exclude_columns > test-annotate-external.R: 2. filter_nonproductive > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-annotate-external.R: v Preprocessing plan is ready > test-annotate-external.R: > test-annotate-external.R: -- Aggregating the data to receptors > test-annotate-external.R: i No locus information found > test-annotate-external.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/file3968a86dc60638/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a86dc60638/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a86dc60638] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a86dc60638'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a86dc60638'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.05 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-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/RtmpnmmaPx/file3968d7c5f670f/annotations.parquet] > test-annotate-external.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d7c5f670f/metadata.json] > test-annotate-external.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d7c5f670f] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d7c5f670f'] > test-annotate-external.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d7c5f670f'] > test-annotate-external.R: > test-annotate-external.R: -- Summary > test-annotate-external.R: i Time elapsed: 3.06 secs > test-annotate-external.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-external.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-agg-strata.R: v Postprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Saving the newly created ImmunData to disk > test-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/file3968a8903fb38/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a8903fb38/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a8903fb38] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a8903fb38'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a8903fb38'] > 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-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/RtmpnmmaPx/file3968d73fe95d5a/annotations.parquet] > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d73fe95d5a/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d73fe95d5a] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d73fe95d5a'] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d73fe95d5a'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-annotate-receptors.R: i Time elapsed: 3.32 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-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 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/RtmplIpVT4/file3968a839345358/annotations.parquet] > 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/RtmpnmmaPx/file3968d74bde7064/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a839345358/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a839345358] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a839345358'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a839345358'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.22 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/RtmpnmmaPx/file3968d74bde7064/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d74bde7064] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d74bde7064'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d74bde7064'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.05 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Renaming the columns and schemas > test-compute-collect-immundata.R: v Renaming is finished > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Preprocessing the data > test-compute-collect-immundata.R: 1. exclude_columns > test-compute-collect-immundata.R: 2. filter_nonproductive > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-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-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/RtmpnmmaPx/file3968d7676faefe/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-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d7676faefe/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d7676faefe] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d7676faefe'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d7676faefe'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.59 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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/RtmplIpVT4/file3968a84fac034f/annotations.parquet] > 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: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a84fac034f/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a84fac034f] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a84fac034f'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a84fac034f'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.08 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-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-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/RtmpnmmaPx/file3968d73389dbf1/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-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d73389dbf1/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d73389dbf1] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d73389dbf1'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d73389dbf1'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.47 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: Rows: 2 Columns: 4 > test-compute-collect-immundata.R: -- Column specification -------------------------------------------------------- > test-compute-collect-immundata.R: Delimiter: "\t" > test-compute-collect-immundata.R: chr (4): File, Therapy, Response, Prefix > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-compute-collect-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-compute-collect-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-compute-collect-immundata.R: v Metadata parsed successfully > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Reading repertoire data > test-compute-collect-immundata.R: 1. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-compute-collect-immundata.R: 2. > test-compute-collect-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-compute-collect-immundata.R: i Checking if all files are of the same type > test-compute-collect-immundata.R: v All files have the same extension > test-agg-strata.R: v 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/RtmplIpVT4/file3968a81e368522/annotations.parquet] > 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: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a81e368522/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a81e368522] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a81e368522'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a81e368522'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.09 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-compute-collect-immundata.R: v Preprocessing plan is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Aggregating the data to receptors > test-compute-collect-immundata.R: i No locus information found > test-compute-collect-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-compute-collect-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-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-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/RtmpnmmaPx/file3968d7729137cf/annotations.parquet] > test-compute-collect-immundata.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d7729137cf/metadata.json] > test-compute-collect-immundata.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d7729137cf] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d7729137cf'] > test-compute-collect-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d7729137cf'] > test-compute-collect-immundata.R: > test-compute-collect-immundata.R: -- Summary > test-compute-collect-immundata.R: i Time elapsed: 4.19 secs > test-compute-collect-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-compute-collect-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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-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-agg-strata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/file3968a86441357c/annotations.parquet] > 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: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a86441357c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a86441357c] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a86441357c'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a86441357c'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.02 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-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: Rows: 2 Columns: 4 > test-agg-strata.R: -- Column specification -------------------------------------------------------- > test-agg-strata.R: Delimiter: "\t" > test-agg-strata.R: chr (4): File, Therapy, Response, Prefix > test-agg-strata.R: > test-agg-strata.R: i Use `spec()` to retrieve the full column specification for this data. > test-agg-strata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-agg-strata.R: i Found 2/2 repertoire files from the metadata on the disk > test-agg-strata.R: v Metadata parsed successfully > test-agg-strata.R: > test-agg-strata.R: -- Reading repertoire data > test-agg-strata.R: 1. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-agg-strata.R: 2. > test-agg-strata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-agg-strata.R: i Checking if all files are of the same type > test-agg-strata.R: v All files have the same extension > test-agg-strata.R: > test-agg-strata.R: -- Renaming the columns and schemas > test-agg-strata.R: v Renaming is finished > test-agg-strata.R: > test-agg-strata.R: -- Preprocessing the data > test-agg-strata.R: 1. exclude_columns > test-agg-strata.R: 2. filter_nonproductive > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d72e319c4e/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d72e319c4e/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d72e319c4e] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d72e319c4e'] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d72e319c4e'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 3.12 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-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-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 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/RtmplIpVT4/file3968a87109839c/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a87109839c/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a87109839c] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a87109839c'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a87109839c'] > 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-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/RtmpnmmaPx/file3968d721a17cc8/annotations.parquet] > test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d721a17cc8/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d721a17cc8] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d721a17cc8'] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d721a17cc8'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 3.34 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-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-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/RtmplIpVT4/file3968a819633a19/annotations.parquet] > test-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a819633a19/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a819633a19] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a819633a19'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a819633a19'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.22 secs > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > 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-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d71b158e51/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d71b158e51/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d71b158e51] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d71b158e51'] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d71b158e51'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 3.23 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: 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-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-agg-strata.R: v Preprocessing plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Aggregating the data to receptors > test-agg-strata.R: i No locus information found > test-agg-strata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-agg-strata.R: v Execution plan for receptor data aggregation and annotation is ready > test-agg-strata.R: > test-agg-strata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d71b505c8a/annotations.parquet] > test-agg-strata.R: v Joining plan is ready > test-agg-strata.R: > test-agg-strata.R: -- Postprocessing the data > test-agg-strata.R: 1. prefix_barcodes > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d71b505c8a/metadata.json] > 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/RtmplIpVT4/file3968a83da5cd31/annotations.parquet] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d71b505c8a] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d71b505c8a'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d71b505c8a'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.36 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-agg-strata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a83da5cd31/metadata.json] > test-agg-strata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a83da5cd31] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a83da5cd31'] > test-agg-strata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a83da5cd31'] > test-agg-strata.R: > test-agg-strata.R: -- Summary > test-agg-strata.R: i Time elapsed: 4.19 secs > test-agg-strata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-agg-strata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > 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: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d779cbc934/annotations.parquet] > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d779cbc934/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d779cbc934] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d779cbc934'] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d779cbc934'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.24 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-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/RtmplIpVT4/file3968a812f35efa/annotations.parquet] > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-immundata.R: > test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data. > test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a812f35efa/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a812f35efa] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a812f35efa'] > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a812f35efa'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 3.2 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: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: > test-filter-receptors.R: -- 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-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-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-receptors.R: 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/RtmplIpVT4/file3968a8c60ee1f/annotations.parquet] > 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/RtmpnmmaPx/file3968d727ca6e8e/annotations.parquet] > test-filter-receptors.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a8c60ee1f/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a8c60ee1f] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a8c60ee1f'] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a8c60ee1f'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 3.14 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d727ca6e8e/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d727ca6e8e] > 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-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d727ca6e8e'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d727ca6e8e'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 4.21 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] 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-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata.R: 2. > test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-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/RtmplIpVT4/legacy_v1_3968a830a988ee/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/legacy_v1_3968a830a988ee/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/legacy_v1_3968a830a988ee] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/legacy_v1_3968a830a988ee'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/legacy_v1_3968a830a988ee'] > 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/RtmplIpVT4/legacy_v1_3968a830a988ee'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.44 secs > 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-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > 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-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/file3968d75e8b0a63/annotations.parquet] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpnmmaPx/file3968d75e8b0a63/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/file3968d75e8b0a63] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d75e8b0a63'] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/file3968d75e8b0a63'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.29 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Reading repertoire data > test-io-repertoires-agg-stepwise.R: 1. /tmp/RtmpnmmaPx/file3968d73a6545a4.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/RtmpnmmaPx/test_immundata_3968d75c8b90d4/annotations.parquet] > test-io-repertoires-agg-stepwise.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d75c8b90d4/metadata.json] > test-io-repertoires-agg-stepwise.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d75c8b90d4] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d75c8b90d4'] > test-io-repertoires-agg-stepwise.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d75c8b90d4'] > test-io-repertoires-agg-stepwise.R: > test-io-repertoires-agg-stepwise.R: -- Summary > test-io-repertoires-agg-stepwise.R: i Time elapsed: 0.3 secs > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg-stepwise.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.5 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: > 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/RtmpnmmaPx/file3968d749e521fc.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/RtmpnmmaPx/test_immundata_3968d7277ea0cc/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d7277ea0cc/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d7277ea0cc] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7277ea0cc'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7277ea0cc'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.27 secs > test-io-repertoires-agg.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-agg.R: v Loaded ImmunData with [5] chains and [4] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpnmmaPx/file3968d713565706.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.46 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/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > 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/RtmpnmmaPx/test_immundata_3968d7541b9631/annotations.parquet] > 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-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d7541b9631/metadata.json] > 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-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d7541b9631] > 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-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7541b9631'] > test-io-immundata.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7541b9631'] > test-io-immundata.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.98 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: > 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/RtmpnmmaPx/file3968d72bd3974c.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/RtmpnmmaPx/test_immundata_3968d760a49e33/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d760a49e33/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d760a49e33] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d760a49e33'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d760a49e33'] > 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 [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpnmmaPx/file3968d727b7eac0.tsv > test-io-repertoires-agg.R: i Checking if all files are of the same type > test-io-repertoires-agg.R: v All files have the same extension > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Aggregating the data to receptors > test-io-repertoires-agg.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-agg.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > 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/RtmpnmmaPx/test_immundata_3968d730d7b5c4/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d730d7b5c4/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d730d7b5c4] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d730d7b5c4'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d730d7b5c4'] > 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 [4] chains and [2] receptors > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Reading repertoire data > test-io-repertoires-agg.R: 1. /tmp/RtmpnmmaPx/file3968d72a95bf0a.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/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.64 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-repertoires-agg.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: v Renaming is finished > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-agg.R: i Writing the receptor annotation data to [/tmp/RtmpnmmaPx/test_immundata_3968d75189197d/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d75189197d/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d75189197d] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d75189197d'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d75189197d'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.98 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/RtmpnmmaPx/file3968d74d530329.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 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/RtmplIpVT4/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 [/tmp/RtmpnmmaPx/test_immundata_3968d778623ebf/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.51 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-repertoires-agg.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d778623ebf/metadata.json] > test-io-repertoires-agg.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d778623ebf] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d778623ebf'] > test-io-repertoires-agg.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d778623ebf'] > test-io-repertoires-agg.R: > test-io-repertoires-agg.R: -- Summary > test-io-repertoires-agg.R: i Time elapsed: 0.99 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: 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: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpnmmaPx/file3968d75e48bbc8.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/RtmpnmmaPx/test_immundata_3968d7487345b4/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d7487345b4/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d7487345b4] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7487345b4'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7487345b4'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.3 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/RtmpnmmaPx/file3968d76a955082.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/RtmpnmmaPx/test_immundata_3968d7660c2022/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d7660c2022/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d7660c2022] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7660c2022'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7660c2022'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.29 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-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: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpnmmaPx/file3968d73b7dae5f.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-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found locus pair: IGH and IGL. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 1.44 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/treated/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/treated/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/treated/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/treated/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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/RtmpnmmaPx/test_immundata_3968d78f0e272/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d78f0e272/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d78f0e272] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d78f0e272'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d78f0e272'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > test-io-repertoires-counts.R: v Loaded ImmunData with [6] chains and [2] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpnmmaPx/file3968d79d7c837.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/RtmplIpVT4/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/RtmpnmmaPx/test_immundata_3968d742907cca/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d742907cca/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d742907cca] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d742907cca'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d742907cca'] > test-io-repertoires-counts.R: > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.94 secs > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > 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: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-repertoires-counts.R: v Loaded ImmunData with [2] chains and [1] receptors > 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-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpnmmaPx/file3968d73dc63b86.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 Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/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/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v002'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call")] > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-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/RtmpnmmaPx/test_immundata_3968d74865caf5/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d74865caf5/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d74865caf5] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d74865caf5'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d74865caf5'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1 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/RtmpnmmaPx/file3968d7348c679b.tsv > test-io-repertoires-counts.R: i Checking if all files are of the same type > test-io-repertoires-counts.R: v All files have the same extension > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Aggregating the data to receptors > test-io-repertoires-counts.R: i Found relaxed locus pair: IGH + (IGL|IGK). The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-counts.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-immundata.R: > test-io-immundata.R: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001'] > 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/RtmpnmmaPx/test_immundata_3968d722dfcf52/annotations.parquet] > 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-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d722dfcf52/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d722dfcf52] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d722dfcf52'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d722dfcf52'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.15 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-immundata.R: 2. filter_nonproductive > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpnmmaPx/file3968d7123a755a.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/RtmpnmmaPx/test_immundata_3968d7460cf24e/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d7460cf24e/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d7460cf24e] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7460cf24e'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7460cf24e'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.16 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and IGH] > test-io-repertoires-counts.R: v Loaded ImmunData with [4] chains and [3] receptors > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Reading repertoire data > test-io-repertoires-counts.R: 1. /tmp/RtmpnmmaPx/file3968d76949cfd.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 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 [/tmp/RtmpnmmaPx/test_immundata_3968d75d1e94ed/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d75d1e94ed/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d75d1e94ed] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d75d1e94ed'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d75d1e94ed'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 0.93 secs > test-io-repertoires-counts.R: v Loaded ImmunData with the receptor schema: [c("v_call", "j_call", "junction_aa") and c("IGH", "IGL")] > 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/RtmpnmmaPx/file3968d76949cfd.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/RtmpnmmaPx/test_immundata_3968d7627cbdab/annotations.parquet] > test-io-repertoires-counts.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d7627cbdab/metadata.json] > test-io-repertoires-counts.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d7627cbdab] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7627cbdab'] > test-io-repertoires-counts.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d7627cbdab'] > test-io-repertoires-counts.R: > test-io-repertoires-counts.R: -- Summary > test-io-repertoires-counts.R: i Time elapsed: 1.09 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-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/RtmplIpVT4/file3968a82a520db9/annotations.parquet] > 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: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a82a520db9/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a82a520db9] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a82a520db9'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a82a520db9'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.14 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-immundata.R: > test-io-immundata.R: -- Reading repertoire data > test-io-immundata.R: 1. > test-io-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-immundata.R: i Checking if all files are of the same type > test-io-immundata.R: v All files have the same extension > test-io-immundata.R: > test-io-immundata.R: -- Renaming the columns and schemas > test-io-immundata.R: v Renaming is finished > test-io-immundata.R: > test-io-immundata.R: -- Aggregating the data to receptors > test-io-immundata.R: i No locus information found > test-io-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-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/RtmpnmmaPx/test_immundata_3968d717deb54c/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d717deb54c/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d717deb54c] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d717deb54c'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d717deb54c'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 1.51 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-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: -- Saving the newly created ImmunData to disk > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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/RtmplIpVT4/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/baseline/v001'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectB] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectB'] > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/snapshots/baseline/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/snapshots/baseline/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectB/snapshots/baseline/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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-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/RtmplIpVT4/imd_snap_tests/projectA/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/imd_snap_tests/projectA'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > 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/RtmpnmmaPx/test_immundata_3968d74f5c80ab/annotations.parquet] > test-io-immundata.R: i Time elapsed: 1.52 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-immundata.R: v Loaded ImmunData with [1000] chains and [916] receptors > test-io-immundata.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/ops/v001/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/ops/v001/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/imd_snap_tests/projectA/snapshots/ops/v001] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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-repertoires-files.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d74f5c80ab/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d74f5c80ab] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d74f5c80ab'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d74f5c80ab'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 2.64 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-immundata.R: 2. filter_nonproductive > 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 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/RtmpnmmaPx/test_immundata_3968d764337bd6/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 [/tmp/RtmplIpVT4/file3968a86ced5160/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d764337bd6/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d764337bd6] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d764337bd6'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d764337bd6'] > 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-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a86ced5160/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a86ced5160] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a86ced5160'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a86ced5160'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.22 secs > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > 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-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: > 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-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/RtmplIpVT4/file3968a89d1cde4/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/RtmpnmmaPx/test_immundata_3968d77b1d377d/annotations.parquet] > test-io-immundata.R: i Writing the metadata to [/tmp/RtmplIpVT4/file3968a89d1cde4/metadata.json] > test-io-immundata.R: v ImmunData files saved to [/tmp/RtmplIpVT4/file3968a89d1cde4] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a89d1cde4'] > test-io-immundata.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/file3968a89d1cde4'] > test-io-immundata.R: > test-io-immundata.R: -- Summary > test-io-immundata.R: i Time elapsed: 3.25 secs > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d77b1d377d/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d77b1d377d] > test-io-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d77b1d377d'] > test-io-immundata.R: v Loaded ImmunData with [1902] chains and [1668] receptors > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d77b1d377d'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.5 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: > 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-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-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-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > 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 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/RtmplIpVT4/test-exclude/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmplIpVT4/test-exclude/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test-exclude] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-exclude'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-exclude'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.5 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-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/RtmplIpVT4/test-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/RtmpnmmaPx/test_immundata_3968d752febd04/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmplIpVT4/test-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-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_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: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d752febd04/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d752febd04] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d752febd04'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d752febd04'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.56 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Reading repertoire data > test-io-repertoires-files.R: 1. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-files.R: 2. > test-io-repertoires-files.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires-files.R: i Checking if all files are of the same type > test-io-repertoires-files.R: v All files have the same extension > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Renaming the columns and schemas > test-io-repertoires-files.R: v Renaming is finished > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Aggregating the data to receptors > test-io-repertoires-files.R: i No locus information found > test-io-repertoires-files.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/tmp/RtmplIpVT4/test-exclude-rename/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmplIpVT4/test-exclude-rename/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test-exclude-rename] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-exclude-rename'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-exclude-rename'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 1.53 secs > test-io-repertoires-processing.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires-processing.R: v Loaded ImmunData with [1000] chains and [917] receptors > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Reading repertoire data > test-io-repertoires-processing.R: 1. > test-io-repertoires-processing.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires-processing.R: i Checking if all files are of the same type > test-io-repertoires-processing.R: v All files have the same extension > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Renaming the columns and schemas > test-io-repertoires-processing.R: v Renaming is finished > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Preprocessing the data > test-io-repertoires-processing.R: 1. exclude_columns > test-io-repertoires-processing.R: 2. filter_nonproductive > test-io-repertoires-processing.R: v Preprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-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-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-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/RtmpnmmaPx/test_immundata_3968d729c822b6/annotations.parquet] > test-io-repertoires-files.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d729c822b6/metadata.json] > test-io-repertoires-files.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d729c822b6] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d729c822b6'] > test-io-repertoires-files.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d729c822b6'] > test-io-repertoires-files.R: > test-io-repertoires-files.R: -- Summary > test-io-repertoires-files.R: i Time elapsed: 3.72 secs > test-io-repertoires-files.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires-files.R: v Loaded ImmunData with [2000] chains and [1757] receptors > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Reading repertoire data > test-io-repertoires-schema-paired.R: 1. > test-io-repertoires-schema-paired.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/ig/multiple_ig_loci.tsv.gz > test-io-repertoires-schema-paired.R: i Checking if all files are of the same type > test-io-repertoires-schema-paired.R: v All files have the same extension > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to receptors > test-io-repertoires-schema-paired.R: i Found locus pair: IGH and IGK. The dataset will be pre-filtered to leave chains for these loci only > test-io-repertoires-schema-paired.R: i Processing data as single-cell sequencing immune repertoires - no counts, with barcodes, chain pairing is possible > test-io-repertoires-processing.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Postprocessing the data > test-io-repertoires-processing.R: 1. prefix_barcodes > test-io-repertoires-processing.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires-processing.R: v Postprocessing plan is ready > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Saving the newly created ImmunData to disk > test-io-repertoires-processing.R: i Writing the receptor annotation data to [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/immundata-sample_0_1k/annotations.parquet] > test-io-repertoires-processing.R: 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/RtmplIpVT4/test_immundata_3968a867b793ca/annotations.parquet] > test-io-repertoires-processing.R: i Writing the metadata to [/tmp/RtmplIpVT4/test_immundata_3968a867b793ca/metadata.json] > test-io-repertoires-processing.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test_immundata_3968a867b793ca] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a867b793ca'] > test-io-repertoires-processing.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a867b793ca'] > test-io-repertoires-processing.R: > test-io-repertoires-processing.R: -- Summary > test-io-repertoires-processing.R: i Time elapsed: 16.91 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: 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/RtmpnmmaPx/test_immundata_3968d77eed767f/annotations.parquet] > 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/RtmplIpVT4/test_immundata_3968a87530d929/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmplIpVT4/test_immundata_3968a87530d929/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test_immundata_3968a87530d929] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a87530d929'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a87530d929'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 3.7 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/RtmplIpVT4/file3968a810f05e18.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/RtmplIpVT4/test_immundata_3968a871fade1c/annotations.parquet] > test-io-repertoires-schema-single.R: i Writing the metadata to [/tmp/RtmplIpVT4/test_immundata_3968a871fade1c/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test_immundata_3968a871fade1c] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a871fade1c'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a871fade1c'] > test-io-repertoires-schema-single.R: > test-io-repertoires-schema-single.R: -- Summary > test-io-repertoires-schema-single.R: i Time elapsed: 0.26 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/RtmplIpVT4/file3968a817016bc4.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-paired.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d77eed767f/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d77eed767f] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d77eed767f'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d77eed767f'] > 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: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 22.13 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-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/RtmplIpVT4/test_immundata_3968a8585a9a4/annotations.parquet] > 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-single.R: i Writing the metadata to [/tmp/RtmplIpVT4/test_immundata_3968a8585a9a4/metadata.json] > test-io-repertoires-schema-single.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test_immundata_3968a8585a9a4] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a8585a9a4'] > test-io-repertoires-schema-single.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test_immundata_3968a8585a9a4'] > 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-paired.R: > test-io-repertoires-schema-paired.R: -- Aggregating the data to 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-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-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/RtmplIpVT4/test-no-barcodes/annotations.parquet] > test-io-repertoires-schema-table.R: i Writing the metadata to [/tmp/RtmplIpVT4/test-no-barcodes/metadata.json] > test-io-repertoires-schema-table.R: v ImmunData files saved to [/tmp/RtmplIpVT4/test-no-barcodes] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/test-no-barcodes'] > test-io-repertoires-schema-table.R: i Reading ImmunData files from ['/tmp/RtmplIpVT4/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: 1.87 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/RtmpnmmaPx/test_immundata_3968d721cec7e6/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d721cec7e6/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d721cec7e6] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d721cec7e6'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d721cec7e6'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 22.79 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/RtmpnmmaPx/file3968d73912ef83.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/RtmpnmmaPx/test_immundata_3968d74ae9b52/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d74ae9b52/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d74ae9b52] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d74ae9b52'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d74ae9b52'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1 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/RtmpnmmaPx/file3968d7662a0011.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/RtmpnmmaPx/test_immundata_3968d774dba822/annotations.parquet] > test-io-repertoires-schema-paired.R: i Writing the metadata to [/tmp/RtmpnmmaPx/test_immundata_3968d774dba822/metadata.json] > test-io-repertoires-schema-paired.R: v ImmunData files saved to [/tmp/RtmpnmmaPx/test_immundata_3968d774dba822] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d774dba822'] > test-io-repertoires-schema-paired.R: i Reading ImmunData files from ['/tmp/RtmpnmmaPx/test_immundata_3968d774dba822'] > test-io-repertoires-schema-paired.R: > test-io-repertoires-schema-paired.R: -- Summary > test-io-repertoires-schema-paired.R: i Time elapsed: 1.04 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: 0.0.5
Check: tests
Result: ERROR Running 'testthat.R' [52s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.5 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-receptors.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-barcodes.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Preprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Aggregating the data to receptors > test-annotate-barcodes.R: i No locus information found > test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.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-receptors.R: > test-annotate-receptors.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-receptors.R: 1. prefix_barcodes > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\RtmpSKYIKr\file132bc23e56d88/annotations.parquet] > 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 [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\file1263c6ca85f3f/annotations.parquet] Saving _problems/test-annotate-barcodes-2.R Saving _problems/test-annotate-receptors-2.R > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.6\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-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-exact.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-barcodes.R: > test-filter-barcodes.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-immundata-exact.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-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Postprocessing the data > test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\RtmpSKYIKr\file132bc60d13ef8/annotations.parquet] > 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 [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\file1263c5f54f6f/annotations.parquet] Saving _problems/test-filter-barcodes-4.R Saving _problems/test-filter-immundata-exact-2.R > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.6\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-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Renaming is finished > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Preprocessing the data > test-filter-immundata-hamm.R: 1. exclude_columns > test-filter-immundata-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-hamm.R: 2. filter_nonproductive > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\RtmpSKYIKr\file132bc4da31429/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\file1263c128e3168/annotations.parquet] Saving _problems/test-filter-immundata-hamm-3.R > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. D:\RCompile\CRANpkg\lib\4.6\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: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.6\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-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: 2. filter_nonproductive > 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-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: 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 [D:\temp\2026_03_10_01_50_00_7065\RtmpSKYIKr\file132bc113c412c/annotations.parquet] > test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Postprocessing the data > test-filter-immundata-lev.R: 1. prefix_barcodes > test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-lev.R: v Postprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-lev.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\file1263c392c60a2/annotations.parquet] Saving _problems/test-filter-immundata-regex-2.R Saving _problems/test-filter-immundata-lev-3.R Saving _problems/test-filter-immundata-lev-29.R > test-filter-immundata.R: Rows: 2 Columns: 4 > test-filter-immundata.R: -- Column specification -------------------------------------------------------- > test-filter-immundata.R: Delimiter: "\t" > test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > 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-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk > test-filter-receptors.R: v All files have the same extension > test-filter-immundata.R: v Metadata parsed successfully > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.6\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-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-immundata.R: > test-filter-immundata.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-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: 2. filter_nonproductive > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-receptors.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\file1263c1d662dd4/annotations.parquet] Saving _problems/test-filter-receptors-3.R > 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-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-filter-immundata.R: 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 [D:\temp\2026_03_10_01_50_00_7065\RtmpSKYIKr\file132bc20205a2f/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\RtmpSKYIKr\file132bc5bf261ef/annotations.parquet] Saving _problems/test-filter-immundata-2.R Saving _problems/test-filter-immundata-20.R > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L/annotations.parquet] > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\test-no-barcodes/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\test-exclude/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: v_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\test-rename/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: j_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_10_01_50_00_7065\Rtmpg5Im2L\test-exclude-rename/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors Saving _problems/test-io-repertoires-28.R Saving _problems/test-io-repertoires-56.R Saving _problems/test-io-repertoires-83.R Saving _problems/test-io-repertoires-120.R Saving _problems/test-io-repertoires-146.R Saving _problems/test-io-repertoires-176.R [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-annotate-barcodes.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-annotate-receptors.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-barcodes.R:4:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-exact.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-hamm.R:3:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-regex.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-lev.R:3:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-lev.R:29:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-receptors.R:3:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_with_metadata() at test-filter-immundata.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata.R:20:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:23:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:51:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:79:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:113:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:141:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:168:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 0.0.5
Check: tests
Result: ERROR Running 'testthat.R' [50s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.5 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-receptors.R: > test-annotate-receptors.R: -- Reading repertoire data > test-annotate-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-annotate-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: v Renaming is finished > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Preprocessing the data > test-annotate-barcodes.R: 1. exclude_columns > test-annotate-receptors.R: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-barcodes.R: 2. filter_nonproductive > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.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-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Postprocessing the data > test-annotate-barcodes.R: 1. prefix_barcodes > test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-barcodes.R: v Postprocessing plan is ready > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk > test-annotate-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\RtmpUlETJz\filefbf86b062ac5/annotations.parquet] > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\file66f45abc33a3/annotations.parquet] Saving _problems/test-annotate-barcodes-2.R > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-filter-barcodes.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.5\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 Saving _problems/test-annotate-receptors-2.R > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-exact.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: > 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-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 [D:\temp\2026_03_06_11_10_10_4045\RtmpUlETJz\filefbf838695ed2/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 [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\file66f46f9f1130/annotations.parquet] Saving _problems/test-filter-barcodes-4.R > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Reading repertoire data > test-filter-immundata-hamm.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.5\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 Saving _problems/test-filter-immundata-exact-2.R > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-hamm.R: 2. filter_nonproductive > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-hamm.R: v Preprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Aggregating the data to receptors > test-filter-immundata-hamm.R: i No locus information found > test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\RtmpUlETJz\filefbf818ff1b17/annotations.parquet] Saving _problems/test-filter-immundata-hamm-3.R > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-regex.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-lev.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: v All files have the same extension > 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 [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\file66f433856385/annotations.parquet] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.5\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 [D:\temp\2026_03_06_11_10_10_4045\RtmpUlETJz\filefbf832c36874/annotations.parquet] Saving _problems/test-filter-immundata-regex-2.R > 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 [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\file66f43dd3351b/annotations.parquet] > 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. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\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 Saving _problems/test-filter-immundata-lev-3.R Saving _problems/test-filter-immundata-lev-29.R > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.5\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-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 [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\file66f44cf71c3/annotations.parquet] > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes Saving _problems/test-filter-receptors-3.R > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\RtmpUlETJz\filefbf858ec278d/annotations.parquet] > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-filter-immundata.R: i Checking if all files are of the same type > test-filter-immundata.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-filter-immundata.R: > test-filter-immundata.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-io-repertoires.R: 2. filter_nonproductive > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\RtmpUlETJz\filefbf820ac1141/annotations.parquet] Saving _problems/test-filter-immundata-2.R Saving _problems/test-filter-immundata-20.R > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J/annotations.parquet] > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: 2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\test-no-barcodes/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\test-exclude/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: v_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\test-rename/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: j_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_06_11_10_10_4045\Rtmpia994J\test-exclude-rename/annotations.parquet] > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors Saving _problems/test-io-repertoires-28.R Saving _problems/test-io-repertoires-56.R Saving _problems/test-io-repertoires-83.R Saving _problems/test-io-repertoires-120.R Saving _problems/test-io-repertoires-146.R Saving _problems/test-io-repertoires-176.R [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-annotate-barcodes.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-annotate-receptors.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-barcodes.R:4:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-exact.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-hamm.R:3:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-regex.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-lev.R:3:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-lev.R:29:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-receptors.R:3:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_with_metadata() at test-filter-immundata.R:2:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata.R:20:3 2. │ └─immundata::read_repertoires(...) 3. │ └─immundata::write_immundata(idata, output_folder) 4. │ ├─duckplyr::compute_parquet(...) 5. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 7. │ └─duckplyr::read_file_duckdb(...) 8. │ └─duckplyr:::duckfun(...) 9. │ └─duckdb$rel_from_table_function(...) 10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 11. │ ├─rlang::try_fetch(...) 12. │ │ ├─base::tryCatch(...) 13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 16. │ │ └─base::withCallingHandlers(...) 17. │ └─duckdb:::rapi_rel_from_table_function(...) 18. └─base::.handleSimpleError(...) 19. └─rlang (local) h(simpleError(msg, call)) 20. └─handlers[[1L]](cnd) 21. └─duckdb:::rethrow_error_from_rapi(e, call) 22. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:23:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:51:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:79:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:113:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:141:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) ── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ── Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"} Backtrace: ▆ 1. ├─immundata::read_repertoires(...) at test-io-repertoires.R:168:3 2. │ └─immundata::write_immundata(idata, output_folder) 3. │ ├─duckplyr::compute_parquet(...) 4. │ └─duckplyr:::compute_parquet.duckplyr_df(...) 5. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options) 6. │ └─duckplyr::read_file_duckdb(...) 7. │ └─duckplyr:::duckfun(...) 8. │ └─duckdb$rel_from_table_function(...) 9. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...) 10. │ ├─rlang::try_fetch(...) 11. │ │ ├─base::tryCatch(...) 12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ │ └─base::withCallingHandlers(...) 16. │ └─duckdb:::rapi_rel_from_table_function(...) 17. └─base::.handleSimpleError(...) 18. └─rlang (local) h(simpleError(msg, call)) 19. └─handlers[[1L]](cnd) 20. └─duckdb:::rethrow_error_from_rapi(e, call) 21. └─rlang::abort(msg, call = call) [ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ] Error: ! Test failures. Execution halted Flavor: r-release-windows-x86_64

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