Check results for 'immundata'

using R Under development (unstable) (2026-03-11 r89605)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-15 (Debian 15.2.0-14) 15.2.0 GNU Fortran (Debian 15.2.0-14) 15.2.0
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8 * current time: 2026-03-12 15:54:36 UTC
checking for file ‘immundata/DESCRIPTION’ ... OK
this is package ‘immundata’ version ‘0.0.5’
package encoding: UTF-8
checking CRAN incoming feasibility ... [2s/2s] OK
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘immundata’ can be installed ... OK See the install log for details.
checking package directory ... OK
checking for future file timestamps ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [2s/2s] OK
checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
checking whether the package can be unloaded cleanly ... [2s/2s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
checking loading without being on the library search path ... [2s/2s] OK
checking whether startup messages can be suppressed ... [2s/2s] OK
checking use of S3 registration ... OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [11s/14s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd line widths ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking examples ... [2s/2s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [63s/40s] ERROR Running ‘testthat.R’ [63s/40s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(immundata) Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: duckplyr The duckplyr package is configured to fall back to dplyr when it encounters an incompatibility. Fallback events can be collected and uploaded for analysis to guide future development. By default, data will be collected but no data will be uploaded. ℹ Automatic fallback uploading is not controlled and therefore disabled, see `?duckplyr::fallback()`. ✔ Number of reports ready for upload: 1. → Review with `duckplyr::fallback_review()`, upload with `duckplyr::fallback_upload()`. ℹ Configure automatic uploading with `duckplyr::fallback_config()`. ✔ Overwriting dplyr methods with duckplyr methods. ℹ Turn off with `duckplyr::methods_restore()`. Loading immundata version 0.0.5 > > test_check("immundata") Starting 2 test processes. > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Reading repertoire data > test-annotate-barcodes.R: 1. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-barcodes.R: 2. > test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-barcodes.R: i Checking if all files are of the same type > test-annotate-barcodes.R: v All files have the same extension > test-annotate-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: -- Reading repertoire data > test-annotate-receptors.R: 1. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-annotate-receptors.R: 2. > test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-annotate-receptors.R: i Checking if all files are of the same type > test-annotate-receptors.R: v All files have the same extension > test-annotate-barcodes.R: 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: > test-annotate-receptors.R: -- Renaming the columns and schemas > test-annotate-receptors.R: v Renaming is finished > test-annotate-receptors.R: > test-annotate-receptors.R: -- Preprocessing the data > test-annotate-receptors.R: 1. exclude_columns > test-annotate-receptors.R: 2. filter_nonproductive > test-annotate-receptors.R: v Preprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Aggregating the data to receptors > test-annotate-receptors.R: i No locus information found > test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-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/Rtmp4kcikj/file3b37c87dd73ec2/annotations.parquet] > test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Postprocessing the data > test-annotate-receptors.R: 1. prefix_barcodes > test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-annotate-receptors.R: v Postprocessing plan is ready > test-annotate-receptors.R: > test-annotate-receptors.R: -- Saving the newly created ImmunData to disk > test-annotate-receptors.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/file3b3820502c2dd1/annotations.parquet] > test-annotate-barcodes.R: i Writing the metadata to [/tmp/Rtmp4kcikj/file3b37c87dd73ec2/metadata.json] > test-annotate-barcodes.R: v ImmunData files saved to [/tmp/Rtmp4kcikj/file3b37c87dd73ec2] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c87dd73ec2'] > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c87dd73ec2'] > test-annotate-barcodes.R: > test-annotate-barcodes.R: -- Summary > test-annotate-barcodes.R: i Time elapsed: 3.26 secs > test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-barcodes.R: v Loaded ImmunData with [1902] chains > test-filter-barcodes.R: > test-filter-barcodes.R: -- Reading repertoire data > test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpJNd2wu/file3b3820502c2dd1/metadata.json] > test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/file3b3820502c2dd1] > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b3820502c2dd1'] > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-barcodes.R: 1. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-barcodes.R: 2. > test-filter-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-barcodes.R: i Checking if all files are of the same type > test-filter-barcodes.R: v All files have the same extension > test-filter-barcodes.R: > test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b3820502c2dd1'] > test-annotate-receptors.R: > test-annotate-receptors.R: -- Summary > test-filter-barcodes.R: -- Renaming the columns and schemas > test-annotate-receptors.R: i Time elapsed: 3.35 secs > test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-annotate-receptors.R: v Loaded ImmunData with [1902] chains > test-filter-barcodes.R: v Renaming is finished > test-filter-barcodes.R: > test-filter-barcodes.R: -- Preprocessing the data > test-filter-barcodes.R: 1. exclude_columns > test-filter-barcodes.R: 2. filter_nonproductive > test-filter-barcodes.R: v Preprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Aggregating the data to receptors > test-filter-barcodes.R: i No locus information found > test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Reading repertoire data > test-filter-immundata-exact.R: 1. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-exact.R: 2. > test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-exact.R: i Checking if all files are of the same type > test-filter-immundata-exact.R: v All files have the same extension > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Renaming the columns and schemas > test-filter-immundata-exact.R: v Renaming is finished > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Preprocessing the data > test-filter-immundata-exact.R: 1. exclude_columns > test-filter-immundata-exact.R: 2. filter_nonproductive > test-filter-immundata-exact.R: v Preprocessing plan is ready > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Aggregating the data to receptors > test-filter-immundata-exact.R: i No locus information found > test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Postprocessing the data > test-filter-barcodes.R: 1. prefix_barcodes > test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-barcodes.R: v Postprocessing plan is ready > test-filter-barcodes.R: > test-filter-barcodes.R: -- Saving the newly created ImmunData to disk > test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmp4kcikj/file3b37c8e2ade4a/annotations.parquet] > test-filter-barcodes.R: i Writing the metadata to [/tmp/Rtmp4kcikj/file3b37c8e2ade4a/metadata.json] > test-filter-barcodes.R: v ImmunData files saved to [/tmp/Rtmp4kcikj/file3b37c8e2ade4a] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c8e2ade4a'] > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c8e2ade4a'] > test-filter-barcodes.R: > test-filter-barcodes.R: -- Summary > test-filter-barcodes.R: i Time elapsed: 2.91 secs > test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-barcodes.R: v Loaded ImmunData with [1902] chains > test-filter-immundata-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/RtmpJNd2wu/file3b3820639fb7fb/annotations.parquet] > 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-exact.R: i Writing the metadata to [/tmp/RtmpJNd2wu/file3b3820639fb7fb/metadata.json] > test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/file3b3820639fb7fb] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b3820639fb7fb'] > test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b3820639fb7fb'] > test-filter-immundata-exact.R: > test-filter-immundata-exact.R: -- Summary > test-filter-immundata-exact.R: i Time elapsed: 2.98 secs > 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-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-exact.R: v Loaded ImmunData with [1902] chains > test-filter-immundata-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: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Postprocessing the data > test-filter-immundata-hamm.R: 1. prefix_barcodes > test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-hamm.R: v Postprocessing plan is ready > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/Rtmp4kcikj/file3b37c839db5a95/annotations.parquet] > test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/Rtmp4kcikj/file3b37c839db5a95/metadata.json] > test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/Rtmp4kcikj/file3b37c839db5a95] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c839db5a95'] > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c839db5a95'] > test-filter-immundata-hamm.R: > test-filter-immundata-hamm.R: -- Summary > test-filter-immundata-hamm.R: i Time elapsed: 2.92 secs > test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-hamm.R: v Loaded ImmunData with [1902] chains > test-filter-immundata-lev.R: 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/RtmpJNd2wu/file3b382024e32e1f/annotations.parquet] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Reading repertoire data > test-filter-immundata-regex.R: 1. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-regex.R: 2. > test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-regex.R: i Checking if all files are of the same type > test-filter-immundata-regex.R: v All files have the same extension > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Renaming the columns and schemas > test-filter-immundata-regex.R: v Renaming is finished > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Preprocessing the data > test-filter-immundata-regex.R: 1. exclude_columns > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpJNd2wu/file3b382024e32e1f/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/file3b382024e32e1f] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b382024e32e1f'] > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b382024e32e1f'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 2.9 secs > test-filter-immundata-regex.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains > test-filter-immundata-regex.R: v Preprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Aggregating the data to receptors > test-filter-immundata-regex.R: i No locus information found > test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Reading repertoire data > test-filter-immundata-lev.R: 1. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-immundata-lev.R: 2. > test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-immundata-lev.R: i Checking if all files are of the same type > test-filter-immundata-lev.R: v All files have the same extension > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Renaming the columns and schemas > test-filter-immundata-lev.R: v Renaming is finished > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Preprocessing the data > test-filter-immundata-lev.R: 1. exclude_columns > test-filter-immundata-lev.R: 2. filter_nonproductive > test-filter-immundata-lev.R: v Preprocessing plan is ready > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Aggregating the data to receptors > test-filter-immundata-lev.R: i No locus information found > test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Postprocessing the data > test-filter-immundata-regex.R: 1. prefix_barcodes > test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata-regex.R: v Postprocessing plan is ready > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk > test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmp4kcikj/file3b37c82941573f/annotations.parquet] > test-filter-immundata-regex.R: i Writing the metadata to [/tmp/Rtmp4kcikj/file3b37c82941573f/metadata.json] > test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/Rtmp4kcikj/file3b37c82941573f] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c82941573f'] > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c82941573f'] > test-filter-immundata-regex.R: > test-filter-immundata-regex.R: -- Summary > test-filter-immundata-regex.R: i Time elapsed: 2.92 secs > test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-regex.R: v Loaded ImmunData with [1902] chains > test-filter-immundata.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-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/RtmpJNd2wu/file3b3820690d66d/annotations.parquet] > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpJNd2wu/file3b3820690d66d/metadata.json] > test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/file3b3820690d66d] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b3820690d66d'] > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b3820690d66d'] > test-filter-immundata-lev.R: > test-filter-immundata-lev.R: -- Summary > test-filter-immundata-lev.R: i Time elapsed: 3.06 secs > test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata-lev.R: v Loaded ImmunData with [1902] chains Saving _problems/test-filter-immundata-lev-24.R > test-filter-receptors.R: > test-filter-receptors.R: -- Reading repertoire data > test-filter-receptors.R: 1. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-filter-receptors.R: 2. > test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-filter-receptors.R: i Checking if all files are of the same type > test-filter-receptors.R: v All files have the same extension > test-filter-receptors.R: > test-filter-receptors.R: -- Renaming the columns and schemas > test-filter-receptors.R: v Renaming is finished > test-filter-receptors.R: > test-filter-receptors.R: -- Preprocessing the data > test-filter-receptors.R: 1. exclude_columns > test-filter-receptors.R: 2. filter_nonproductive > test-filter-receptors.R: v Preprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Aggregating the data to receptors > test-filter-receptors.R: i No locus information found > test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column > test-filter-immundata.R: v Joining plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp4kcikj/file3b37c867b6864/annotations.parquet] > test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Postprocessing the data > test-filter-receptors.R: 1. prefix_barcodes > test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-receptors.R: v Postprocessing plan is ready > test-filter-receptors.R: > test-filter-receptors.R: -- Saving the newly created ImmunData to disk > test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/file3b38204c49c0fe/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmp4kcikj/file3b37c867b6864/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmp4kcikj/file3b37c867b6864] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c867b6864'] > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c867b6864'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 3.84 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains > test-filter-immundata.R: > test-filter-immundata.R: -- Reading repertoire data > test-filter-immundata.R: 1. > test-filter-immundata.R: /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-receptors.R: i Writing the metadata to [/tmp/RtmpJNd2wu/file3b38204c49c0fe/metadata.json] > test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/file3b38204c49c0fe] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b38204c49c0fe'] > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/file3b38204c49c0fe'] > test-filter-receptors.R: > test-filter-receptors.R: -- Summary > test-filter-receptors.R: i Time elapsed: 3.02 secs > test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-receptors.R: v Loaded ImmunData with [1902] chains > test-filter-immundata.R: v Renaming is finished > test-filter-immundata.R: > test-filter-immundata.R: -- Preprocessing the data > test-filter-immundata.R: 1. exclude_columns > test-filter-immundata.R: 2. filter_nonproductive > test-filter-immundata.R: v Preprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Aggregating the data to receptors > test-filter-immundata.R: i No locus information found > test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: 2. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Postprocessing the data > test-filter-immundata.R: 1. prefix_barcodes > test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-filter-immundata.R: v Postprocessing plan is ready > test-filter-immundata.R: > test-filter-immundata.R: -- Saving the newly created ImmunData to disk > test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmp4kcikj/file3b37c85a3a574e/annotations.parquet] > test-filter-immundata.R: i Writing the metadata to [/tmp/Rtmp4kcikj/file3b37c85a3a574e/metadata.json] > test-filter-immundata.R: v ImmunData files saved to [/tmp/Rtmp4kcikj/file3b37c85a3a574e] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c85a3a574e'] > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-filter-immundata.R: i Reading ImmunData files from ['/tmp/Rtmp4kcikj/file3b37c85a3a574e'] > test-filter-immundata.R: > test-filter-immundata.R: -- Summary > test-filter-immundata.R: i Time elapsed: 2.96 secs > test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-filter-immundata.R: v Loaded ImmunData with [1902] chains > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJNd2wu/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJNd2wu] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 4.08 secs > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires.R: v Loaded ImmunData with [1902] chains > test-io-repertoires.R: Rows: 2 Columns: 4 > test-io-repertoires.R: -- Column specification -------------------------------------------------------- > test-io-repertoires.R: Delimiter: "\t" > test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix > test-io-repertoires.R: > test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data. > test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message. > test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk > test-io-repertoires.R: v Metadata parsed successfully > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: 2. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column > test-io-repertoires.R: v Joining plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJNd2wu/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJNd2wu] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 4.09 secs > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires.R: v Loaded ImmunData with [1902] chains > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/test-no-barcodes/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJNd2wu/test-no-barcodes/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/test-no-barcodes] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-no-barcodes'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-no-barcodes'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.66 secs > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires.R: v Loaded ImmunData with [955] chains > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/test-exclude/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJNd2wu/test-exclude/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/test-exclude] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-exclude'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-exclude'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.71 secs > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and NULL] > test-io-repertoires.R: v Loaded ImmunData with [1000] chains > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: v_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/test-rename/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJNd2wu/test-rename/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/test-rename] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-rename'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-rename'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.73 secs > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and NULL] > test-io-repertoires.R: v Loaded ImmunData with [955] chains > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Introduced new renamed columns: j_gene > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors > test-io-repertoires.R: i No locus information found > test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible > test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Postprocessing the data > test-io-repertoires.R: 1. prefix_barcodes > test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing > test-io-repertoires.R: v Postprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Saving the newly created ImmunData to disk > test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpJNd2wu/test-exclude-rename/annotations.parquet] > test-io-repertoires.R: i Writing the metadata to [/tmp/RtmpJNd2wu/test-exclude-rename/metadata.json] > test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmpJNd2wu/test-exclude-rename] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-exclude-rename'] > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()] > test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmpJNd2wu/test-exclude-rename'] > test-io-repertoires.R: > test-io-repertoires.R: -- Summary > test-io-repertoires.R: i Time elapsed: 1.7 secs > test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and NULL] > test-io-repertoires.R: v Loaded ImmunData with [1000] chains > test-io-repertoires.R: > test-io-repertoires.R: -- Reading repertoire data > test-io-repertoires.R: 1. > test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv > test-io-repertoires.R: i Checking if all files are of the same type > test-io-repertoires.R: v All files have the same extension > test-io-repertoires.R: > test-io-repertoires.R: -- Renaming the columns and schemas > test-io-repertoires.R: v Renaming is finished > test-io-repertoires.R: > test-io-repertoires.R: -- Preprocessing the data > test-io-repertoires.R: 1. exclude_columns > test-io-repertoires.R: 2. filter_nonproductive > test-io-repertoires.R: v Preprocessing plan is ready > test-io-repertoires.R: > test-io-repertoires.R: -- Aggregating the data to receptors [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-filter-immundata-lev.R:21:3'): Levenshtein fuzzy matching returns correct results ── Expected `arrange(collect(out$receptors))` to equal `arrange(gold)`. Differences: `attr(actual, 'row.names')`: NA -3 `attr(expected, 'row.names')`: 1 2 3 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ] Error: ! Test failures. Execution halted
checking PDF version of manual ... [4s/5s] OK
checking HTML version of manual ... [2s/3s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 1 ERROR