Last updated on 2026-03-06 20:52:30 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.5 | 11.15 | 228.27 | 239.42 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.0.5 | 7.91 | 118.39 | 126.30 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.5 | 19.00 | 333.32 | 352.32 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.0.5 | 20.00 | 283.46 | 303.46 | ERROR | |
| r-devel-macos-arm64 | 0.0.5 | 3.00 | 43.00 | 46.00 | OK | |
| r-devel-windows-x86_64 | 0.0.5 | 14.00 | 147.00 | 161.00 | ERROR | |
| r-patched-linux-x86_64 | 0.0.5 | 11.30 | 169.12 | 180.42 | ERROR | |
| r-release-linux-x86_64 | 0.0.5 | 11.44 | 168.39 | 179.83 | ERROR | |
| r-release-macos-arm64 | 0.0.5 | OK | ||||
| r-release-macos-x86_64 | 0.0.5 | 8.00 | 191.00 | 199.00 | OK | |
| r-release-windows-x86_64 | 0.0.5 | 14.00 | 147.00 | 161.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.0.5 | OK | ||||
| r-oldrel-macos-x86_64 | 0.0.5 | 7.00 | 169.00 | 176.00 | OK | |
| r-oldrel-windows-x86_64 | 0.0.5 | 17.00 | 190.00 | 207.00 | ERROR |
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [133s/85s]
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-clang/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-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-barcodes.R: i Checking if all files are of the same type
> test-annotate-barcodes.R: v All files have the same extension
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Reading repertoire data
> test-annotate-receptors.R: 1.
> test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-clang/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-clang/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-barcodes.R:
> test-annotate-barcodes.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-barcodes.R: v Renaming is finished
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Preprocessing the data
> test-annotate-receptors.R: 1. exclude_columns
> test-annotate-barcodes.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-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: -- Aggregating the data to receptors
> test-annotate-receptors.R: i No locus information found
> test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Postprocessing the data
> test-annotate-barcodes.R: 1. prefix_barcodes
> test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-barcodes.R: v Postprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk
> test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp4z824h/file11033131a83eb0/annotations.parquet]
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Postprocessing the data
> test-annotate-receptors.R: 1. prefix_barcodes
> test-annotate-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-receptors.R: v Postprocessing plan is ready
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Saving the newly created ImmunData to disk
> test-annotate-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpL8tQmr/file11033c68db0a5/annotations.parquet]
Saving _problems/test-annotate-receptors-2.R
Saving _problems/test-annotate-barcodes-2.R
> 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-clang/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-clang/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-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-clang/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-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-exact.R: i Checking if all files are of the same type
> test-filter-immundata-exact.R: v All files have the same extension
> test-filter-barcodes.R:
> 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-barcodes.R:
> test-filter-barcodes.R: -- Saving the newly created ImmunData to disk
> test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpL8tQmr/file11033c390182d2/annotations.parquet]
> test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Postprocessing the data
> test-filter-immundata-exact.R: 1. prefix_barcodes
> test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmp4z824h/file1103312c84fe27/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.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-clang/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-clang/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
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.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-clang/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-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-hamm.R: v 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:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-hamm.R: 2. filter_nonproductive
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-hamm.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> 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: 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 [/home/hornik/tmp/scratch/RtmpL8tQmr/file11033c24dfde5e/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 [/home/hornik/tmp/scratch/Rtmp4z824h/file11033123ec6d34/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.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-clang/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-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R:
> 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-clang/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-clang/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-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 [/home/hornik/tmp/scratch/RtmpL8tQmr/file11033c18e1766c/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 [/home/hornik/tmp/scratch/Rtmp4z824h/file1103315902b465/annotations.parquet]
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R:
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FAL
> test-filter-immundata.R: SE` 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-clang/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-clang/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
Saving _problems/test-filter-immundata-lev-3.R
Saving _problems/test-filter-immundata-lev-29.R
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> 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-clang/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-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-immundata.R: v 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:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R: 2. filter_nonproductive
> 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 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: 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 [/home/hornik/tmp/scratch/Rtmp4z824h/file110331900f022/annotations.parquet]
Saving _problems/test-filter-receptors-3.R
> 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-clang/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-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-filter-immundata.R: 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:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Postprocessing plan is ready
> test-io-repertoires.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpL8tQmr/file11033c13f4e7ad/annotations.parquet]
> 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.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-clang/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-clang/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-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 [/home/hornik/tmp/scratch/RtmpL8tQmr/file11033c4f2e16b8/annotations.parquet]
> 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 [/home/hornik/tmp/scratch/Rtmp4z824h/annotations.parquet]
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> 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-clang/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-clang/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 [/home/hornik/tmp/scratch/Rtmp4z824h/annotations.parquet]
> 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-clang/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 [/home/hornik/tmp/scratch/Rtmp4z824h/test-no-barcodes/annotations.parquet]
> 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-clang/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-clang/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 [/home/hornik/tmp/scratch/Rtmp4z824h/test-exclude/annotations.parquet]
> 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-clang/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 [/home/hornik/tmp/scratch/Rtmp4z824h/test-rename/annotations.parquet]
> 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-clang/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 [/home/hornik/tmp/scratch/Rtmp4z824h/test-exclude-rename/annotations.parquet]
> 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-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
Saving _problems/test-io-repertoires-28.R
Saving _problems/test-io-repertoires-56.R
Saving _problems/test-io-repertoires-83.R
Saving _problems/test-io-repertoires-120.R
Saving _problems/test-io-repertoires-146.R
Saving _problems/test-io-repertoires-176.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-annotate-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$rel_from_table_function(...)
10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_rel_from_table_function(...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─duckdb:::rethrow_error_from_rapi(e, call)
22. └─rlang::abort(msg, call = call)
── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-annotate-barcodes.R:2:3
2. │ └─immundata::read_repertoires(...)
3. │ └─immundata::write_immundata(idata, output_folder)
4. │ ├─duckplyr::compute_parquet(...)
5. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
7. │ └─duckplyr::read_file_duckdb(...)
8. │ └─duckplyr:::duckfun(...)
9. │ └─duckdb$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-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-linux-x86_64-debian-clang
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [57s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(immundata)
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: duckplyr
The duckplyr package is configured to fall back to dplyr when it encounters an
incompatibility. Fallback events can be collected and uploaded for analysis to
guide future development. By default, data will be collected but no data will
be uploaded.
ℹ Automatic fallback uploading is not controlled and therefore disabled, see
`?duckplyr::fallback()`.
✔ Number of reports ready for upload: 1.
→ Review with `duckplyr::fallback_review()`, upload with
`duckplyr::fallback_upload()`.
ℹ Configure automatic uploading with `duckplyr::fallback_config()`.
✔ Overwriting dplyr methods with duckplyr methods.
ℹ Turn off with `duckplyr::methods_restore()`.
Loading immundata version 0.0.5
>
> test_check("immundata")
Starting 2 test processes.
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Reading repertoire data
> test-annotate-barcodes.R: 1.
> test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-barcodes.R: 2.
> test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-barcodes.R: i Checking if all files are of the same type
> test-annotate-barcodes.R: v All files have the same extension
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Reading repertoire data
> test-annotate-receptors.R: 1.
> test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-receptors.R: 2.
> test-annotate-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-receptors.R: i Checking if all files are of the same type
> test-annotate-receptors.R: v All files have the same extension
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Renaming the columns and schemas
> test-annotate-barcodes.R: v Renaming is finished
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Preprocessing the data
> test-annotate-barcodes.R: 1. exclude_columns
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Renaming the columns and schemas
> test-annotate-barcodes.R: 2. filter_nonproductive
> test-annotate-receptors.R: v Renaming is finished
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Preprocessing the data
> test-annotate-receptors.R: 1. exclude_columns
> test-annotate-barcodes.R: v Preprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Aggregating the data to receptors
> test-annotate-barcodes.R: i No locus information found
> test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-receptors.R: 2. filter_nonproductive
> test-annotate-receptors.R: v Preprocessing plan is ready
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Aggregating the data to receptors
> test-annotate-receptors.R: i No locus information found
> test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Postprocessing the data
> test-annotate-barcodes.R: 1. prefix_barcodes
> test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-barcodes.R: v Postprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk
> test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmphECnCG/file3edc3a931533f/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/RtmpS2uPzT/file3edc13334bc88d/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.
> 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-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1.
> test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-exact.R: 2.
> test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-exact.R: i Checking if all files are of the same type
> test-filter-immundata-exact.R: v All files have the same extension
> test-filter-barcodes.R:
> 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-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/RtmpS2uPzT/file3edc13197e0285/annotations.parquet]
> 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/RtmphECnCG/file3edc3a5571a533/annotations.parquet]
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.
> 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
Saving _problems/test-filter-barcodes-4.R
> 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: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-hamm.R: v 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:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-hamm.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-hamm.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R: 2. filter_nonproductive
> 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 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/RtmpS2uPzT/file3edc131f0778e7/annotations.parquet]
> test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Postprocessing the data
> test-filter-immundata-lev.R: 1. prefix_barcodes
> test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-lev.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmphECnCG/file3edc3a3bc002fb/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.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-regex.R: 2.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> 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-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-lev.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 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/RtmpS2uPzT/file3edc13989c04e/annotations.parquet]
> test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Postprocessing the data
> test-filter-immundata-lev.R: 1. prefix_barcodes
> test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-lev.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/RtmphECnCG/file3edc3a1501bf43/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-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-receptors.R: 1.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-receptors.R: 2.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-immundata.R: 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: -- Renaming the columns and schemas
> 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-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-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-receptors.R: v Preprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Aggregating the data to receptors
> test-filter-receptors.R: i No locus information found
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-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/RtmphECnCG/file3edc3a4c71602a/annotations.parquet]
> 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
Saving _problems/test-filter-receptors-3.R
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: 2.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-filter-immundata.R: 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:
> 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-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/RtmpS2uPzT/file3edc1371c2dfb2/annotations.parquet]
> 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.
> 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-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-io-repertoires.R: v Joining plan is ready
> test-io-repertoires.R:
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: -- Postprocessing the data
> test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpS2uPzT/file3edc137ab052b7/annotations.parquet]
> 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/RtmphECnCG/annotations.parquet]
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> 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/RtmphECnCG/annotations.parquet]
> 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/RtmphECnCG/test-no-barcodes/annotations.parquet]
> 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/RtmphECnCG/test-exclude/annotations.parquet]
> 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/RtmphECnCG/test-rename/annotations.parquet]
> 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/RtmphECnCG/test-exclude-rename/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
Saving _problems/test-io-repertoires-28.R
Saving _problems/test-io-repertoires-56.R
Saving _problems/test-io-repertoires-83.R
Saving _problems/test-io-repertoires-120.R
Saving _problems/test-io-repertoires-146.R
Saving _problems/test-io-repertoires-176.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
Error in `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$rel_from_table_function(...)
10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_rel_from_table_function(...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─duckdb:::rethrow_error_from_rapi(e, call)
22. └─rlang::abort(msg, call = call)
── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ──
Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-exact.R:2:3
2. │ └─immundata::read_repertoires(...)
3. │ └─immundata::write_immundata(idata, output_folder)
4. │ ├─duckplyr::compute_parquet(...)
5. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
7. │ └─duckplyr::read_file_duckdb(...)
8. │ └─duckplyr:::duckfun(...)
9. │ └─duckdb$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-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$rel_from_table_function(...)
10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_rel_from_table_function(...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─duckdb:::rethrow_error_from_rapi(e, call)
22. └─rlang::abort(msg, call = call)
── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ──
Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-hamm.R:3:3
2. │ └─immundata::read_repertoires(...)
3. │ └─immundata::write_immundata(idata, output_folder)
4. │ ├─duckplyr::compute_parquet(...)
5. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
7. │ └─duckplyr::read_file_duckdb(...)
8. │ └─duckplyr:::duckfun(...)
9. │ └─duckdb$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-linux-x86_64-debian-gcc
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [196s/173s]
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: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-barcodes.R: 2.
> test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-barcodes.R: i Checking if all files are of the same type
> test-annotate-barcodes.R: v All files have the same extension
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Reading repertoire data
> test-annotate-receptors.R: 1.
> test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-receptors.R: 2.
> test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-receptors.R: i Checking if all files are of the same type
> test-annotate-receptors.R: v All files have the same extension
> test-annotate-barcodes.R:
> 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-barcodes.R:
> test-annotate-barcodes.R: -- Preprocessing the data
> test-annotate-barcodes.R: 1. exclude_columns
> test-annotate-receptors.R: v Renaming is finished
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Preprocessing the data
> test-annotate-receptors.R: 1. exclude_columns
> test-annotate-barcodes.R: 2. filter_nonproductive
> 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 [/tmp/Rtmpd6zbSG/working_dir/RtmpprBxlE/file3852213734a35/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/Rtmpd6zbSG/working_dir/RtmpCzzeJm/file38523ab2dfc8/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.
> test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-barcodes.R: 2.
> test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-barcodes.R: i Checking if all files are of the same type
> test-filter-barcodes.R: v All files have the same extension
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Renaming the columns and schemas
Saving _problems/test-annotate-receptors-2.R
> test-filter-barcodes.R: v Renaming is finished
> test-filter-immundata-exact.R:
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-barcodes.R: 1. exclude_columns
> test-filter-immundata-exact.R: 1.
> test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-exact.R: 2.
> test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-exact.R: i Checking if all files are of the same type
> test-filter-immundata-exact.R: v All files have the same extension
> test-filter-barcodes.R: 2. filter_nonproductive
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: v Preprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Aggregating the data to receptors
> test-filter-barcodes.R: i No locus information found
> test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-exact.R: v Renaming is finished
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Preprocessing the data
> test-filter-immundata-exact.R: 1. exclude_columns
> test-filter-immundata-exact.R: 2. filter_nonproductive
> test-filter-immundata-exact.R: v Preprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Aggregating the data to receptors
> test-filter-immundata-exact.R: i No locus information found
> test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Postprocessing the data
> test-filter-barcodes.R: 1. prefix_barcodes
> test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-barcodes.R: v Postprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Saving the newly created ImmunData to disk
> test-filter-barcodes.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpprBxlE/file38522dffd31e/annotations.parquet]
> test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Postprocessing the data
> test-filter-immundata-exact.R: 1. prefix_barcodes
> test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/file38523119d288f/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.
> test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-hamm.R: 2.
> test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-hamm.R: i Checking if all files are of the same type
> test-filter-immundata-hamm.R: v All files have the same extension
Saving _problems/test-filter-immundata-exact-2.R
> 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: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-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:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-hamm.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-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: 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/Rtmpd6zbSG/working_dir/RtmpprBxlE/file385227b2f92e0/annotations.parquet]
> test-filter-immundata-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Postprocessing the data
> test-filter-immundata-lev.R: 1. prefix_barcodes
> test-filter-immundata-lev.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-lev.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-lev.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/file3852358ed9445/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.
> test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-regex.R: 2.
> test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-regex.R: 2. filter_nonproductive
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R: v Preprocessing plan is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Aggregating the data to receptors
> test-filter-immundata-regex.R: i No locus information found
> test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> test-filter-immundata-lev.R: 2. filter_nonproductive
> test-filter-immundata-lev.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Aggregating the data to receptors
> test-filter-immundata-lev.R: i No locus information found
> test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Postprocessing the data
> test-filter-immundata-regex.R: 1. prefix_barcodes
> test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-regex.R: v Postprocessing plan is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-regex.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpprBxlE/file3852253f8427f/annotations.parquet]
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Respons
> test-filter-immundata.R: e, 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 = FAL
> test-filter-immundata.R: SE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-filter-immundata-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/Rtmpd6zbSG/working_dir/RtmpCzzeJm/file385235e9d6f7c/annotations.parquet]
> 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
Saving _problems/test-filter-immundata-lev-3.R
Saving _problems/test-filter-immundata-lev-29.R
> test-filter-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-receptors.R: 1.
> test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-receptors.R: 2.
> test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R:
> test-filter-receptors.R: -- Preprocessing the data
> test-filter-receptors.R: 1. exclude_columns
> test-filter-receptors.R: 2. filter_nonproductive
> test-filter-receptors.R: v Preprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Aggregating the data to receptors
> test-filter-receptors.R: i No locus information found
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column
> test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Postprocessing the data
> test-filter-receptors.R: 1. prefix_barcodes
> test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-receptors.R: v Postprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Saving the newly created ImmunData to disk
> test-filter-receptors.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/file385237d1347a6/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 [/tmp/Rtmpd6zbSG/working_dir/RtmpprBxlE/file3852240979329/annotations.parquet]
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: 2.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Postprocessing the data
> test-filter-immundata.R: 1. prefix_barcodes
> test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata.R: v Postprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpprBxlE/file385225ce5e76e/annotations.parquet]
> 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/Rtmpd6zbSG/working_dir/RtmpCzzeJm/annotations.parquet]
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: 2.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column
> test-io-repertoires.R: v Joining plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/test-no-barcodes/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/test-exclude/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Introduced new renamed columns: v_gene
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/test-rename/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Introduced new renamed columns: j_gene
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/Rtmpd6zbSG/working_dir/RtmpCzzeJm/test-exclude-rename/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-clang/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
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-linux-x86_64-fedora-clang
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [143s/214s]
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: 3.
→ Review with `duckplyr::fallback_review()`, upload with
`duckplyr::fallback_upload()`.
ℹ Configure automatic uploading with `duckplyr::fallback_config()`.
✔ Overwriting dplyr methods with duckplyr methods.
ℹ Turn off with `duckplyr::methods_restore()`.
Loading immundata version 0.0.5
>
> test_check("immundata")
Starting 2 test processes.
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Reading repertoire data
> test-annotate-barcodes.R: 1.
> test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-barcodes.R: 2.
> test-annotate-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Reading repertoire data
> 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: 1.
> test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-receptors.R: 2.
> test-annotate-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-receptors.R: i Checking if all files are of the same type
> test-annotate-receptors.R: v All files have the same extension
> test-annotate-barcodes.R:
> 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-barcodes.R: v Preprocessing plan is ready
> test-annotate-receptors.R: 1. exclude_columns
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Aggregating the data to receptors
> test-annotate-barcodes.R: i No locus information found
> test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-receptors.R: 2. filter_nonproductive
> test-annotate-receptors.R: v Preprocessing plan is ready
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Aggregating the data to receptors
> test-annotate-receptors.R: i No locus information found
> test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Postprocessing the data
> test-annotate-barcodes.R: 1. prefix_barcodes
> test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-barcodes.R: v Postprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk
> test-annotate-barcodes.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/file275c5b1bb93242/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/RtmpqmG2S2/working_dir/Rtmpto2MnZ/file275c5e7fd0e976/annotations.parquet]
Saving _problems/test-annotate-receptors-2.R
Saving _problems/test-annotate-barcodes-2.R
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Reading repertoire data
> test-filter-barcodes.R: 1.
> test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-barcodes.R: 2.
> test-filter-barcodes.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-barcodes.R: i Checking if all files are of the same type
> test-filter-barcodes.R: v All files have the same extension
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1.
> test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-exact.R: 2.
> test-filter-immundata-exact.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-exact.R: i Checking if all files are of the same type
> test-filter-immundata-exact.R: v All files have the same extension
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: v Renaming is finished
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-barcodes.R: 1. exclude_columns
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- 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-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: 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/RtmpqmG2S2/working_dir/Rtmpto2MnZ/file275c5e58c06b56/annotations.parquet]
> test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Postprocessing the data
> test-filter-immundata-exact.R: 1. prefix_barcodes
> test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/file275c5b929eb36/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.
> test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-hamm.R: 2.
> test-filter-immundata-hamm.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-hamm.R: i Checking if all files are of the same type
> test-filter-immundata-hamm.R: v All files have the same extension
> test-filter-immundata-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
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.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> test-filter-immundata-lev.R: 2. filter_nonproductive
> test-filter-immundata-lev.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Aggregating the data to receptors
> test-filter-immundata-lev.R: i No locus information found
> test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-hamm.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Postprocessing the data
> test-filter-immundata-hamm.R: 1. prefix_barcodes
> test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-hamm.R: v Postprocessing plan is ready
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/Rtmpto2MnZ/file275c5e50c2af1b/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.
> test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-regex.R: 2.
> test-filter-immundata-regex.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-regex.R: 2. filter_nonproductive
> test-filter-immundata-regex.R: v Preprocessing plan is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Aggregating the data to receptors
> test-filter-immundata-regex.R: i No locus information found
> test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-lev.R: 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/RtmpqmG2S2/working_dir/RtmpdSeCsw/file275c5b2af43915/annotations.parquet]
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-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/RtmpqmG2S2/working_dir/Rtmpto2MnZ/file275c5e4f1ccad1/annotations.parquet]
> 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
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R:
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-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/RtmpqmG2S2/working_dir/RtmpdSeCsw/file275c5b3e052465/annotations.parquet]
> 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
Saving _problems/test-filter-immundata-lev-3.R
Saving _problems/test-filter-immundata-lev-29.R
> test-filter-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-receptors.R: 1.
> test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-receptors.R: 2.
> test-filter-receptors.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Joining plan is ready
> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R:
> test-filter-immundata.R:
> test-filter-immundata.R: -- Postprocessing the data
> test-filter-receptors.R: -- Preprocessing the data
> test-filter-immundata.R: 1. prefix_barcodes
> 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-immundata.R: v Postprocessing 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-immundata.R:
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/Rtmpto2MnZ/file275c5e45589f30/annotations.parquet]
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-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/RtmpqmG2S2/working_dir/RtmpdSeCsw/file275c5b5c660a33/annotations.parquet]
Saving _problems/test-filter-receptors-3.R
> 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, Respons
> test-io-repertoires.R: e, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: 2.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Postprocessing the data
> test-filter-immundata.R: 1. prefix_barcodes
> test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata.R: v Postprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/Rtmpto2MnZ/file275c5e96b99d3/annotations.parquet]
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> 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/RtmpqmG2S2/working_dir/RtmpdSeCsw/annotations.parquet]
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: 2.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column
> test-io-repertoires.R: v Joining plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/test-no-barcodes/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/test-exclude/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Introduced new renamed columns: v_gene
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/test-rename/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Introduced new renamed columns: j_gene
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmpqmG2S2/working_dir/RtmpdSeCsw/test-exclude-rename/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /data/gannet/ripley/R/packages/tests-devel/immundata.Rcheck/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
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-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-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$rel_from_table_function(...)
10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_rel_from_table_function(...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─duckdb:::rethrow_error_from_rapi(e, call)
22. └─rlang::abort(msg, call = call)
── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ──
Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-barcodes.R:4:3
2. │ └─immundata::read_repertoires(...)
3. │ └─immundata::write_immundata(idata, output_folder)
4. │ ├─duckplyr::compute_parquet(...)
5. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
7. │ └─duckplyr::read_file_duckdb(...)
8. │ └─duckplyr:::duckfun(...)
9. │ └─duckdb$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-linux-x86_64-fedora-gcc
Version: 0.0.5
Check: tests
Result: ERROR
Running 'testthat.R' [51s]
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-barcodes.R:
> test-annotate-barcodes.R: -- Preprocessing the data
> test-annotate-barcodes.R: 1. exclude_columns
> test-annotate-receptors.R: v Renaming is finished
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Preprocessing the data
> test-annotate-receptors.R: 1. exclude_columns
> test-annotate-barcodes.R: 2. filter_nonproductive
> 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_03_01_50_00_30890\Rtmpis2JpG\filebd545f1f41d8/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_03_01_50_00_30890\Rtmpg1PYLV\filed9e035765ad3/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-immundata-exact.R: 2. filter_nonproductive
> test-filter-barcodes.R: 2. filter_nonproductive
> test-filter-immundata-exact.R: v Preprocessing plan is ready
> test-filter-barcodes.R: v Preprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Aggregating the data to receptors
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Aggregating the data to receptors
> test-filter-barcodes.R: i No locus information found
> test-filter-immundata-exact.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: 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_03_01_50_00_30890\Rtmpis2JpG\filebd541a877557/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_03_01_50_00_30890\Rtmpg1PYLV\filed9e0579e5a12/annotations.parquet]
Saving _problems/test-filter-barcodes-4.R
Saving _problems/test-filter-immundata-exact-2.R
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.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-hamm.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata-lev.R: v All files have the same extension
> 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: -- Renaming the columns and schemas
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.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-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-lev.R: 2. filter_nonproductive
> test-filter-immundata-hamm.R: v Preprocessing plan is ready
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Aggregating the data to receptors
> test-filter-immundata-hamm.R: i No locus information found
> test-filter-immundata-hamm.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-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-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-hamm.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Postprocessing the data
> test-filter-immundata-hamm.R: v Postprocessing plan is ready
> test-filter-immundata-lev.R: 1. prefix_barcodes
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Saving the newly created ImmunData to disk
> 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-hamm.R: i Writing the receptor annotation data to [D:\temp\2026_03_03_01_50_00_30890\Rtmpis2JpG\filebd542b61ce0/annotations.parquet]
> 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_03_01_50_00_30890\Rtmpg1PYLV\filed9e057955a43/annotations.parquet]
> 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
Saving _problems/test-filter-immundata-hamm-3.R
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> 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-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:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R: 2. filter_nonproductive
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-regex.R: 2. filter_nonproductive
> test-filter-immundata-lev.R: v 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 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-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-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-regex.R: i Writing the receptor annotation data to [D:\temp\2026_03_03_01_50_00_30890\Rtmpis2JpG\filebd546cf72256/annotations.parquet]
> 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_03_01_50_00_30890\Rtmpg1PYLV\filed9e0605260be/annotations.parquet]
Saving _problems/test-filter-immundata-lev-3.R
Saving _problems/test-filter-immundata-lev-29.R
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> 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-receptors.R: v All files have the same extension
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R:
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R:
> test-filter-receptors.R: -- Preprocessing the data
> test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-receptors.R: 1. exclude_columns
> 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-receptors.R: 2. filter_nonproductive
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-receptors.R: v Preprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Aggregating the data to receptors
> test-filter-receptors.R: i No locus information found
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-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_03_01_50_00_30890\Rtmpis2JpG\filebd5478f2509/annotations.parquet]
> 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
Saving _problems/test-filter-receptors-3.R
> 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 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:
> 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-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_03_01_50_00_30890\Rtmpg1PYLV\filed9e04ada62d0/annotations.parquet]
> 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_03_01_50_00_30890\Rtmpg1PYLV\filed9e02d8b694f/annotations.parquet]
> 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_03_01_50_00_30890\Rtmpis2JpG/annotations.parquet]
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> 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_03_01_50_00_30890\Rtmpis2JpG/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_03_01_50_00_30890\Rtmpis2JpG\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_03_01_50_00_30890\Rtmpis2JpG\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_03_01_50_00_30890\Rtmpis2JpG\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_03_01_50_00_30890\Rtmpis2JpG\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$rel_from_table_function(...)
10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_rel_from_table_function(...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─duckdb:::rethrow_error_from_rapi(e, call)
22. └─rlang::abort(msg, call = call)
── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ──
Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-lev.R:3:3
2. │ └─immundata::read_repertoires(...)
3. │ └─immundata::write_immundata(idata, output_folder)
4. │ ├─duckplyr::compute_parquet(...)
5. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
7. │ └─duckplyr::read_file_duckdb(...)
8. │ └─duckplyr:::duckfun(...)
9. │ └─duckdb$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$rel_from_table_function(...)
10. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
11. │ ├─rlang::try_fetch(...)
12. │ │ ├─base::tryCatch(...)
13. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
16. │ │ └─base::withCallingHandlers(...)
17. │ └─duckdb:::rapi_rel_from_table_function(...)
18. └─base::.handleSimpleError(...)
19. └─rlang (local) h(simpleError(msg, call))
20. └─handlers[[1L]](cnd)
21. └─duckdb:::rethrow_error_from_rapi(e, call)
22. └─rlang::abort(msg, call = call)
── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ──
Error in `duckfun(table_function, c(list(path), options), prudence = prudence, remote = remote)`: {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata:::get_test_idata_tsv_no_metadata() at test-filter-immundata-regex.R:2:3
2. │ └─immundata::read_repertoires(...)
3. │ └─immundata::write_immundata(idata, output_folder)
4. │ ├─duckplyr::compute_parquet(...)
5. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
6. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
7. │ └─duckplyr::read_file_duckdb(...)
8. │ └─duckplyr:::duckfun(...)
9. │ └─duckdb$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-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’ [88s/59s]
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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-barcodes.R: 2.
> test-annotate-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-barcodes.R: i Checking if all files are of the same type
> test-annotate-barcodes.R: v All files have the same extension
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Reading repertoire data
> test-annotate-receptors.R: 1.
> test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-annotate-receptors.R: 2.
> test-annotate-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-receptors.R: i Checking if all files are of the same type
> test-annotate-receptors.R: v All files have the same extension
> test-annotate-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-barcodes.R: 2. filter_nonproductive
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Renaming the columns and schemas
> 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 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 [/home/hornik/tmp/scratch/RtmpazDsPu/file243e73ae9fd20/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 [/home/hornik/tmp/scratch/RtmpCvJqi4/file243e7b1c43d5aa/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.
> test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-barcodes.R: 2.
> test-filter-barcodes.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-barcodes.R: i Checking if all files are of the same type
> test-filter-barcodes.R: v All files have the same extension
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: v Renaming is finished
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-barcodes.R: 1. exclude_columns
Saving _problems/test-annotate-receptors-2.R
> test-filter-barcodes.R: 2. filter_nonproductive
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1.
> test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-exact.R: 2.
> test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-exact.R: i Checking if all files are of the same type
> test-filter-immundata-exact.R: v All files have the same extension
> test-filter-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 [/home/hornik/tmp/scratch/RtmpazDsPu/file243e734221cf2a/annotations.parquet]
> test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Postprocessing the data
> test-filter-immundata-exact.R: 1. prefix_barcodes
> test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpCvJqi4/file243e7b23b75044/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.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-hamm.R: 2.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-hamm.R: i Checking if all files are of the same type
> test-filter-immundata-hamm.R: v All files have the same extension
> test-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
Saving _problems/test-filter-immundata-exact-2.R
> 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:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> test-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 [/home/hornik/tmp/scratch/RtmpazDsPu/file243e737cc2330d/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 [/home/hornik/tmp/scratch/RtmpCvJqi4/file243e7b2b6c6c65/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.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-regex.R: 2.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-lev.R: 2.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-lev.R: i Checking if all files are of the same type
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-regex.R: 2. filter_nonproductive
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R: v Preprocessing plan is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Aggregating the data to receptors
> test-filter-immundata-regex.R: i No locus information found
> test-filter-immundata-regex.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> test-filter-immundata-lev.R: 2. filter_nonproductive
> test-filter-immundata-lev.R: v Preprocessing plan is ready
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Aggregating the data to receptors
> test-filter-immundata-lev.R: i No locus information found
> test-filter-immundata-lev.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-regex.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Postprocessing the data
> test-filter-immundata-regex.R: 1. prefix_barcodes
> test-filter-immundata-regex.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-regex.R: v Postprocessing plan is ready
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-regex.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpazDsPu/file243e7321af8273/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 [/home/hornik/tmp/scratch/RtmpCvJqi4/file243e7b5b3cbcae/annotations.parquet]
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R:
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
Saving _problems/test-filter-immundata-lev-3.R
Saving _problems/test-filter-immundata-lev-29.R
> 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:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-receptors.R: 1.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-receptors.R: 2.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-receptors.R: v 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 [/home/hornik/tmp/scratch/RtmpCvJqi4/file243e7b196c1b26/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 [/home/hornik/tmp/scratch/RtmpazDsPu/file243e73764225a7/annotations.parquet]
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-patched-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-patched-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-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-io-repertoires.R: 2. filter_nonproductive
> 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-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: 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 [/home/hornik/tmp/scratch/RtmpazDsPu/file243e7398a5164/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 [/home/hornik/tmp/scratch/RtmpCvJqi4/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, Respons
> test-io-repertoires.R: e, 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-patched-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-patched-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 [/home/hornik/tmp/scratch/RtmpCvJqi4/annotations.parquet]
> 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-patched-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 [/home/hornik/tmp/scratch/RtmpCvJqi4/test-no-barcodes/annotations.parquet]
> 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-patched-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-patched-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 [/home/hornik/tmp/scratch/RtmpCvJqi4/test-exclude/annotations.parquet]
> 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-patched-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 [/home/hornik/tmp/scratch/RtmpCvJqi4/test-rename/annotations.parquet]
> 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-patched-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 [/home/hornik/tmp/scratch/RtmpCvJqi4/test-exclude-rename/annotations.parquet]
> 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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
Saving _problems/test-io-repertoires-28.R
Saving _problems/test-io-repertoires-56.R
Saving _problems/test-io-repertoires-83.R
Saving _problems/test-io-repertoires-120.R
Saving _problems/test-io-repertoires-146.R
Saving _problems/test-io-repertoires-176.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
Error in `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-patched-linux-x86_64
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [87s/57s]
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-release-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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-barcodes.R: i Checking if all files are of the same type
> test-annotate-barcodes.R: v All files have the same extension
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Reading repertoire data
> test-annotate-receptors.R: 1.
> test-annotate-receptors.R: /home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-annotate-receptors.R: i Checking if all files are of the same type
> test-annotate-receptors.R: v All files have the same extension
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Renaming the columns and schemas
> test-annotate-barcodes.R: v Renaming is finished
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Preprocessing the data
> test-annotate-barcodes.R: 1. exclude_columns
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Renaming the columns and schemas
> test-annotate-barcodes.R: 2. filter_nonproductive
> test-annotate-receptors.R: v Renaming is finished
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Preprocessing the data
> test-annotate-receptors.R: 1. exclude_columns
> test-annotate-barcodes.R: v Preprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Aggregating the data to receptors
> test-annotate-barcodes.R: i No locus information found
> test-annotate-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-receptors.R: 2. filter_nonproductive
> test-annotate-receptors.R: v Preprocessing plan is ready
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Aggregating the data to receptors
> test-annotate-receptors.R: i No locus information found
> test-annotate-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-annotate-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Postprocessing the data
> test-annotate-barcodes.R: 1. prefix_barcodes
> test-annotate-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-annotate-barcodes.R: v Postprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Saving the newly created ImmunData to disk
> test-annotate-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpPBbDeR/file26f42a42c3eafa/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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/file26f42f5044a19b/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.
> test-filter-barcodes.R: /home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-barcodes.R: i Checking if all files are of the same type
> test-filter-barcodes.R: v All files have the same extension
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: v Renaming is finished
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-barcodes.R: 1. exclude_columns
Saving _problems/test-annotate-receptors-2.R
> test-filter-barcodes.R: 2. filter_nonproductive
> 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-release-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-release-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-barcodes.R: v Preprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Aggregating the data to receptors
> test-filter-immundata-exact.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: i No locus information found
> test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-exact.R: v Renaming is finished
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Preprocessing the data
> test-filter-immundata-exact.R: 1. exclude_columns
> test-filter-immundata-exact.R: 2. filter_nonproductive
> test-filter-immundata-exact.R: v Preprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Aggregating the data to receptors
> test-filter-immundata-exact.R: i No locus information found
> test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Postprocessing the data
> test-filter-barcodes.R: 1. prefix_barcodes
> test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-barcodes.R: v Postprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Saving the newly created ImmunData to disk
> test-filter-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpPBbDeR/file26f42a64347f63/annotations.parquet]
> test-filter-immundata-exact.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Postprocessing the data
> test-filter-immundata-exact.R: 1. prefix_barcodes
> test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpe0dzpH/file26f42f2044bf1d/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.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-release-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-release-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
Saving _problems/test-filter-immundata-exact-2.R
> 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:
> 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-release-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-release-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 [/home/hornik/tmp/scratch/RtmpPBbDeR/file26f42a32f7a758/annotations.parquet]
Saving _problems/test-filter-immundata-hamm-3.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-regex.R:
> test-filter-immundata-regex.R: -- Reading repertoire data
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-lev.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpe0dzpH/file26f42f7f2fe408/annotations.parquet]
> test-filter-immundata-regex.R: 1.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-release-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-release-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:
> 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-release-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-release-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 [/home/hornik/tmp/scratch/RtmpPBbDeR/file26f42a6c9af7b1/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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/file26f42f16192ff2/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-release-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-release-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
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-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-receptors.R: 1.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R:
> test-filter-receptors.R: -- Preprocessing the data
> test-filter-receptors.R: 1. exclude_columns
> test-filter-receptors.R: 2. filter_nonproductive
> test-filter-receptors.R: v Preprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Aggregating the data to receptors
> test-filter-receptors.R: i No locus information found
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column
> test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Postprocessing the data
> test-filter-receptors.R: 1. prefix_barcodes
> test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-receptors.R: v Postprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Saving the newly created ImmunData to disk
> test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpe0dzpH/file26f42f7605c39e/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 [/home/hornik/tmp/scratch/RtmpPBbDeR/file26f42a3d62c988/annotations.parquet]
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-release-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-release-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-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-release-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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-io-repertoires.R: 2. filter_nonproductive
> 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-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: 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 [/home/hornik/tmp/scratch/RtmpPBbDeR/file26f42a57d072c2/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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/annotations.parquet]
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-release-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-release-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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/annotations.parquet]
> 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-release-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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/test-no-barcodes/annotations.parquet]
> 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-release-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-release-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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/test-exclude/annotations.parquet]
> 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-release-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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/test-rename/annotations.parquet]
> 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-release-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 [/home/hornik/tmp/scratch/Rtmpe0dzpH/test-exclude-rename/annotations.parquet]
> 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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
Saving _problems/test-io-repertoires-28.R
Saving _problems/test-io-repertoires-56.R
Saving _problems/test-io-repertoires-83.R
Saving _problems/test-io-repertoires-120.R
Saving _problems/test-io-repertoires-146.R
Saving _problems/test-io-repertoires-176.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
Error in `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-linux-x86_64
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\4.5\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-barcodes.R: 2. filter_nonproductive
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Renaming the columns and schemas
> test-annotate-barcodes.R: v Preprocessing plan is ready
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Aggregating the data to receptors
> test-annotate-receptors.R: v Renaming is finished
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Preprocessing the data
> 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: 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 [D:\temp\2026_03_04_01_50_00_18124\RtmpAXQs7E\file132804f39814/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_04_01_50_00_18124\Rtmp6nQc63\file96b864d53740/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
Saving _problems/test-annotate-receptors-2.R
> test-filter-barcodes.R: v Renaming is finished
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-barcodes.R: 1. exclude_columns
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1. 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: 2. filter_nonproductive
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: v Preprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Aggregating the data to receptors
> test-filter-barcodes.R: i No locus information found
> test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-exact.R: v Renaming is finished
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Preprocessing the data
> test-filter-immundata-exact.R: 1. exclude_columns
> test-filter-immundata-exact.R: 2. filter_nonproductive
> test-filter-immundata-exact.R: v Preprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Aggregating the data to receptors
> test-filter-immundata-exact.R: i No locus information found
> test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Postprocessing the data
> test-filter-barcodes.R: 1. prefix_barcodes
> test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-barcodes.R: v Postprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Saving the newly created ImmunData to disk
> test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_04_01_50_00_18124\RtmpAXQs7E\file132806fa44cb3/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_04_01_50_00_18124\Rtmp6nQc63\file96b870403adf/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-lev.R: v Renaming is finished
> test-filter-immundata-hamm.R: i No locus information found
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> 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: 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_04_01_50_00_18124\RtmpAXQs7E\file13280310765/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_04_01_50_00_18124\Rtmp6nQc63\file96b8ec35731/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-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\4.5\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-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_04_01_50_00_18124\RtmpAXQs7E\file1328035cf1bd2/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_04_01_50_00_18124\Rtmp6nQc63\file96b8662f23a2/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-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-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-immundata.R: 1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-receptors.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-receptors.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-receptors.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: 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-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-receptors.R: 1. exclude_columns
> test-filter-immundata.R: 1. exclude_columns
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-receptors.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-receptors.R: v Preprocessing plan is ready
> 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: -- 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_04_01_50_00_18124\Rtmp6nQc63\file96b87b2b359a/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\4.5\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: 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_04_01_50_00_18124\RtmpAXQs7E\file13280360d4f56/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-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: 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: -- 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_04_01_50_00_18124\RtmpAXQs7E\file1328069b43fcd/annotations.parquet]
> test-io-repertoires.R: v Joining plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [D:\temp\2026_03_04_01_50_00_18124\Rtmp6nQc63/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_04_01_50_00_18124\Rtmp6nQc63/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_04_01_50_00_18124\Rtmp6nQc63\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_04_01_50_00_18124\Rtmp6nQc63\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_04_01_50_00_18124\Rtmp6nQc63\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_04_01_50_00_18124\Rtmp6nQc63\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: 0.0.5
Check: tests
Result: ERROR
Running 'testthat.R' [72s]
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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.4\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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-annotate-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.4\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-barcodes.R: 2. filter_nonproductive
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Renaming the columns and schemas
> 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 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 [D:\temp\2026_03_04_01_50_00_18124\RtmpOgRFce\file1707047b729a7/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_04_01_50_00_18124\RtmpQXuxM7\file163603d659d/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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-barcodes.R: 2. D:\RCompile\CRANpkg\lib\4.4\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
Saving _problems/test-annotate-receptors-2.R
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Renaming the columns and schemas
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-exact.R: 2. D:\RCompile\CRANpkg\lib\4.4\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 Renaming is finished
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-barcodes.R: 1. exclude_columns
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Renaming the columns and schemas
> test-filter-barcodes.R: 2. filter_nonproductive
> test-filter-immundata-exact.R: v Renaming is finished
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Preprocessing the data
> test-filter-immundata-exact.R: 1. exclude_columns
> test-filter-barcodes.R: v Preprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Aggregating the data to receptors
> test-filter-barcodes.R: i No locus information found
> test-filter-barcodes.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata-exact.R: 2. filter_nonproductive
> test-filter-immundata-exact.R: v Preprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Aggregating the data to receptors
> test-filter-immundata-exact.R: i No locus information found
> test-filter-immundata-exact.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-barcodes.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Postprocessing the data
> test-filter-barcodes.R: 1. prefix_barcodes
> test-filter-barcodes.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-barcodes.R: v Postprocessing plan is ready
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Saving the newly created ImmunData to disk
> test-filter-barcodes.R: i Writing the receptor annotation data to [D:\temp\2026_03_04_01_50_00_18124\RtmpOgRFce\file170702d896679/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_04_01_50_00_18124\RtmpQXuxM7\file1636030b714ef/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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-hamm.R: 2. D:\RCompile\CRANpkg\lib\4.4\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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.4\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-hamm.R: 2. filter_nonproductive
> test-filter-immundata-lev.R: v All files have the same extension
> test-filter-immundata-hamm.R: v Preprocessing plan is ready
> test-filter-immundata-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:
> 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 [D:\temp\2026_03_04_01_50_00_18124\RtmpOgRFce\file17070710e3f85/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_04_01_50_00_18124\RtmpQXuxM7\file163605bcc774b/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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-regex.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-regex.R: 2. filter_nonproductive
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata-lev.R: 2. D:\RCompile\CRANpkg\lib\4.4\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 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: -- 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_04_01_50_00_18124\RtmpOgRFce\file1707014321a25/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_04_01_50_00_18124\RtmpQXuxM7\file1636033454232/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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\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
Saving _problems/test-filter-immundata-lev-3.R
Saving _problems/test-filter-immundata-lev-29.R
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-receptors.R:
> test-filter-receptors.R: -- Reading repertoire data
> test-filter-receptors.R: 1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-receptors.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R:
> test-filter-receptors.R: -- Preprocessing the data
> test-filter-receptors.R: 1. exclude_columns
> test-filter-receptors.R: 2. filter_nonproductive
> test-filter-receptors.R: v Preprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Aggregating the data to receptors
> test-filter-receptors.R: i No locus information found
> test-filter-receptors.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Joining the metadata table with the dataset using 'filename' column
> test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Postprocessing the data
> test-filter-receptors.R: 1. prefix_barcodes
> test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-receptors.R: v Postprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Saving the newly created ImmunData to disk
> test-filter-receptors.R: i Writing the receptor annotation data to [D:\temp\2026_03_04_01_50_00_18124\RtmpQXuxM7\file1636072347130/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_04_01_50_00_18124\RtmpOgRFce\file170701cdd24f2/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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires.R: 2. D:\RCompile\CRANpkg\lib\4.4\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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-filter-immundata.R: 2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> 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-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-filter-immundata.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> 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_04_01_50_00_18124\RtmpOgRFce\file170704bab7302/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_04_01_50_00_18124\RtmpQXuxM7/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\4.4\immundata\extdata\tsv\sample_0_1k.tsv
> test-io-repertoires.R: 2. D:\RCompile\CRANpkg\lib\4.4\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_04_01_50_00_18124\RtmpQXuxM7/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.4\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_04_01_50_00_18124\RtmpQXuxM7\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\4.4\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\4.4\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_04_01_50_00_18124\RtmpQXuxM7\test-exclude/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.4\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_04_01_50_00_18124\RtmpQXuxM7\test-rename/annotations.parquet]
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1. D:\RCompile\CRANpkg\lib\4.4\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_04_01_50_00_18124\RtmpQXuxM7\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\4.4\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-oldrel-windows-x86_64