Last updated on 2026-02-06 13:50:35 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| immunarch | 4 | 2 | 7 |
| immundata | 4 | 9 |
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpvfhxgw/filea7830237e9322/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/Rtmpvfhxgw/filea7830237e9322/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpvfhxgw/filea7830237e9322]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpvfhxgw/filea7830237e9322']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpvfhxgw/filea7830237e9322']
── Summary
ℹ Time elapsed: 8.65 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/tmp/Rtmpv8FvjG/file22b85c259dd7aa/annotations.parquet]
ℹ Writing the metadata to [/tmp/Rtmpv8FvjG/file22b85c259dd7aa/metadata.json]
✔ ImmunData files saved to [/tmp/Rtmpv8FvjG/file22b85c259dd7aa]
ℹ Reading ImmunData files from ['/tmp/Rtmpv8FvjG/file22b85c259dd7aa']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/Rtmpv8FvjG/file22b85c259dd7aa']
── Summary
ℹ Time elapsed: 3.89 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1.
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpA9VgR0/fileab7aa4862549f/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/RtmpA9VgR0/fileab7aa4862549f/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/RtmpA9VgR0/fileab7aa4862549f]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpA9VgR0/fileab7aa4862549f']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpA9VgR0/fileab7aa4862549f']
── Summary
ℹ Time elapsed: 7.26 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.10.3
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_0_1k.tsv
2. D:\RCompile\CRANpkg\lib\4.4\immundata\extdata\tsv\sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [D:\temp\2026_02_04_01_50_01_15123\RtmpQzYgVE\fileb48019c05a4c/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpQzYgVE\fileb48019c05a4c/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpQzYgVE\fileb48019c05a4c]
ℹ Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpQzYgVE\fileb48019c05a4c']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpQzYgVE\fileb48019c05a4c']
── Summary
ℹ Time elapsed: 6.94 secs
Error in `count()`:
! This operation cannot be carried out by DuckDB, and the input is a
stingy duckplyr frame.
ℹ Use `compute(prudence = "lavish")` to materialize to temporary storage and
continue with duckplyr.
ℹ See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ ├─dplyr::pull(count(idata), "n")
8. │ ├─dplyr::count(idata)
9. │ └─immundata:::count.ImmunData(idata)
10. │ ├─dplyr::count(x$annotations)
11. │ └─duckplyr:::count.duckplyr_df(x$annotations)
12. │ ├─duckplyr:::rel_try(...)
13. │ │ └─rlang::try_fetch(rel, error = identity)
14. │ │ ├─base::tryCatch(...)
15. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
18. │ │ └─base::withCallingHandlers(...)
19. │ └─dplyr:::tally_n(...)
20. │ └─rlang::quo_is_null(wt)
21. └─rlang::abort(message = message)
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: ERROR: 4, OK: 9
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/70s]
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-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-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/Rtmpe0BMb8/filea17803cec0e88/annotations.parquet]
> 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/RtmpITRX7G/filea179c1be52cab/annotations.parquet]
> test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17803cec0e88/metadata.json]
> test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17803cec0e88]
> test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17803cec0e88']
> test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c1be52cab/metadata.json]
> test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c1be52cab]
> test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17803cec0e88']
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Summary
> test-annotate-receptors.R: i Time elapsed: 6.89 secs
> test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c1be52cab']
> test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c1be52cab']
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Summary
> test-annotate-barcodes.R: i Time elapsed: 7.09 secs
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-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-barcodes.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17806ee0148e/annotations.parquet]
> test-filter-immundata-exact.R: 1. prefix_barcodes
> test-filter-immundata-exact.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata-exact.R: v Postprocessing plan is ready
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata-exact.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c4d94dec1/annotations.parquet]
> test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17806ee0148e/metadata.json]
> test-filter-immundata-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c4d94dec1/metadata.json]
> test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c4d94dec1]
> test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17806ee0148e]
> test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17806ee0148e']
> test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c4d94dec1']
> test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17806ee0148e']
> test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c4d94dec1']
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Summary
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Summary
> test-filter-barcodes.R: i Time elapsed: 5.62 secs
> test-filter-immundata-exact.R: i Time elapsed: 5.57 secs
Saving _problems/test-filter-immundata-exact-2.R
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-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:
> test-filter-immundata-hamm.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-hamm.R: v Renaming is finished
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Preprocessing the data
> test-filter-immundata-hamm.R: 1. exclude_columns
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> test-filter-immundata-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-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-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 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/Rtmpe0BMb8/filea17801491da2a/annotations.parquet]
> 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/RtmpITRX7G/filea179c33c02bbe/annotations.parquet]
> test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801491da2a/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801491da2a]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801491da2a']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801491da2a']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c33c02bbe/metadata.json]
> test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c33c02bbe]
> test-filter-immundata-lev.R: i Time elapsed: 5.58 secs
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c33c02bbe']
> test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c33c02bbe']
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Summary
> test-filter-immundata-hamm.R: i Time elapsed: 5.66 secs
> 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
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-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.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-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: 2. filter_nonproductive
> 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-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/Rtmpe0BMb8/filea17801eae0e93/annotations.parquet]
> 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/RtmpITRX7G/filea179c7d0380c9/annotations.parquet]
> test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801eae0e93/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801eae0e93]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801eae0e93']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801eae0e93']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 5.5 secs
> test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c7d0380c9/metadata.json]
> test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c7d0380c9]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c7d0380c9']
> test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c7d0380c9']
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Summary
> test-filter-immundata-regex.R: i Time elapsed: 5.58 secs
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.
> 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: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R:
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-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-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-filter-receptors.R: v Renaming is finished
> test-filter-receptors.R:
> test-filter-receptors.R: -- Preprocessing the data
> test-filter-receptors.R: 1. exclude_columns
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-receptors.R: 2. filter_nonproductive
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-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 Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-receptors.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Postprocessing the data
> test-filter-receptors.R: 1. prefix_barcodes
> test-filter-receptors.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-receptors.R: v Postprocessing plan is ready
> test-filter-receptors.R:
> test-filter-receptors.R: -- Saving the newly created ImmunData to disk
> test-filter-receptors.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c45fa7214/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
> test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c45fa7214/metadata.json]
> test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/filea179c45fa7214]
> test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c45fa7214']
> test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/filea179c45fa7214']
> test-filter-receptors.R:
> test-filter-receptors.R: -- Summary
> test-filter-receptors.R: i Time elapsed: 5.67 secs
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-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 [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801ebdefc7/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: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801ebdefc7/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801ebdefc7]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801ebdefc7']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea17801ebdefc7']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 7.81 secs
> 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-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-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/Rtmpe0BMb8/filea1780732e546e/annotations.parquet]
> 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/RtmpITRX7G/annotations.parquet]
> test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea1780732e546e/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpe0BMb8/filea1780732e546e]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea1780732e546e']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpe0BMb8/filea1780732e546e']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 5.53 secs
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 7.81 secs
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-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/RtmpITRX7G/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 7.87 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-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/RtmpITRX7G/test-no-barcodes/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/test-no-barcodes/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/test-no-barcodes]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-no-barcodes']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-no-barcodes']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.97 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-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/RtmpITRX7G/test-exclude/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.92 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-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/RtmpITRX7G/test-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/test-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/test-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.83 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-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/RtmpITRX7G/test-exclude-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpITRX7G/test-exclude-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.89 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-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 `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [51s/32s]
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-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/RtmplVEmR8/file21b6e04f7f3875/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/RtmpNiy9q6/file21b6c06023a614/annotations.parquet]
> test-annotate-barcodes.R: i Writing the metadata to [/tmp/RtmplVEmR8/file21b6e04f7f3875/metadata.json]
> test-annotate-barcodes.R: v ImmunData files saved to [/tmp/RtmplVEmR8/file21b6e04f7f3875]
> test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e04f7f3875']
> test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-barcodes.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e04f7f3875']
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Summary
> test-annotate-barcodes.R: i Time elapsed: 2.63 secs
> test-annotate-receptors.R: i Writing the metadata to [/tmp/RtmpNiy9q6/file21b6c06023a614/metadata.json]
> test-annotate-receptors.R: v ImmunData files saved to [/tmp/RtmpNiy9q6/file21b6c06023a614]
> test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c06023a614']
> test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-receptors.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c06023a614']
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Summary
> test-annotate-receptors.R: i Time elapsed: 2.58 secs
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-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/RtmplVEmR8/file21b6e0655d89ea/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/RtmpNiy9q6/file21b6c07644bc62/annotations.parquet]
> test-filter-barcodes.R: i Writing the metadata to [/tmp/RtmplVEmR8/file21b6e0655d89ea/metadata.json]
> test-filter-barcodes.R: v ImmunData files saved to [/tmp/RtmplVEmR8/file21b6e0655d89ea]
> test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e0655d89ea']
> test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-barcodes.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e0655d89ea']
> test-filter-immundata-exact.R: i Writing the metadata to [/tmp/RtmpNiy9q6/file21b6c07644bc62/metadata.json]
> test-filter-immundata-exact.R: v ImmunData files saved to [/tmp/RtmpNiy9q6/file21b6c07644bc62]
> test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c07644bc62']
> test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Summary
> test-filter-barcodes.R: i Time elapsed: 2.4 secs
> test-filter-immundata-exact.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c07644bc62']
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Summary
> test-filter-immundata-exact.R: i Time elapsed: 2.37 secs
Saving _problems/test-filter-barcodes-4.R
Saving _problems/test-filter-immundata-exact-2.R
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Reading repertoire data
> test-filter-immundata-hamm.R: 1.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-hamm.R: 2.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-hamm.R: i Checking if all files are of the same type
> test-filter-immundata-hamm.R: v All files have the same extension
> test-filter-immundata-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:
> test-filter-immundata-hamm.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> test-filter-immundata-hamm.R: v Renaming is finished
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Preprocessing the data
> test-filter-immundata-hamm.R: 1. exclude_columns
> test-filter-immundata-lev.R: v Renaming is finished
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 1. exclude_columns
> test-filter-immundata-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-lev.R: v Execution plan for receptor data aggregation and annotation is ready
> 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-lev.R:
> test-filter-immundata-lev.R: -- Postprocessing the data
> test-filter-immundata-lev.R: 1. prefix_barcodes
> test-filter-immundata-hamm.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-hamm.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-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-lev.R: i Writing the receptor annotation data to [/tmp/RtmpNiy9q6/file21b6c02ca3dd28/annotations.parquet]
> test-filter-immundata-hamm.R: i Writing the receptor annotation data to [/tmp/RtmplVEmR8/file21b6e067916de1/annotations.parquet]
> test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpNiy9q6/file21b6c02ca3dd28/metadata.json]
> test-filter-immundata-hamm.R: i Writing the metadata to [/tmp/RtmplVEmR8/file21b6e067916de1/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpNiy9q6/file21b6c02ca3dd28]
> test-filter-immundata-hamm.R: v ImmunData files saved to [/tmp/RtmplVEmR8/file21b6e067916de1]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c02ca3dd28']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e067916de1']
> test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c02ca3dd28']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 2.38 secs
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e067916de1']
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Summary
> test-filter-immundata-hamm.R: i Time elapsed: 2.43 secs
> 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
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: -- Renaming the columns and schemas
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.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-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-lev.R: 2. filter_nonproductive
> 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-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/RtmpNiy9q6/file21b6c0739b2eb1/annotations.parquet]
> 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/RtmplVEmR8/file21b6e0449e4d49/annotations.parquet]
> test-filter-immundata-lev.R: i Writing the metadata to [/tmp/RtmpNiy9q6/file21b6c0739b2eb1/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [/tmp/RtmpNiy9q6/file21b6c0739b2eb1]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c0739b2eb1']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c0739b2eb1']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 2.35 secs
> test-filter-immundata-regex.R: i Writing the metadata to [/tmp/RtmplVEmR8/file21b6e0449e4d49/metadata.json]
> test-filter-immundata-regex.R: v ImmunData files saved to [/tmp/RtmplVEmR8/file21b6e0449e4d49]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e0449e4d49']
> test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e0449e4d49']
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Summary
> test-filter-immundata-regex.R: i Time elapsed: 2.39 secs
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.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-receptors.R: 2.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R: Rows: 2 Columns: 4
> test-filter-immundata.R: -- Column specification --------------------------------------------------------
> test-filter-immundata.R: Delimiter: "\t"
> test-filter-immundata.R: chr (4): File, Therapy, Response, Prefix
> test-filter-immundata.R:
> test-filter-immundata.R: i Use `spec()` to retrieve the full column specification for this data.
> test-filter-immundata.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-filter-immundata.R: i Found 2/2 repertoire files from the metadata on the disk
> test-filter-immundata.R: v Metadata parsed successfully
> test-filter-immundata.R:
> test-filter-immundata.R: -- Reading repertoire data
> test-filter-immundata.R: 1.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata.R: 2.
> test-filter-immundata.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata.R: i Checking if all files are of the same type
> test-filter-immundata.R: v All files have the same extension
> test-filter-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:
> 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 [/tmp/RtmplVEmR8/file21b6e05b545065/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
> test-filter-receptors.R: i Writing the metadata to [/tmp/RtmplVEmR8/file21b6e05b545065/metadata.json]
> test-filter-receptors.R: v ImmunData files saved to [/tmp/RtmplVEmR8/file21b6e05b545065]
> test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e05b545065']
> test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-receptors.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/file21b6e05b545065']
> test-filter-receptors.R:
> test-filter-receptors.R: -- Summary
> test-filter-receptors.R: i Time elapsed: 2.43 secs
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-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/RtmpNiy9q6/file21b6c04aa8bd6f/annotations.parquet]
> 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-filter-immundata.R: i Writing the metadata to [/tmp/RtmpNiy9q6/file21b6c04aa8bd6f/metadata.json]
> 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 ImmunData files saved to [/tmp/RtmpNiy9q6/file21b6c04aa8bd6f]
> test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c04aa8bd6f']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c04aa8bd6f']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 3.18 secs
> 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-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata.R: i Writing the receptor annotation data to [/tmp/RtmpNiy9q6/file21b6c059b01ff/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/RtmplVEmR8/annotations.parquet]
> test-filter-immundata.R: i Writing the metadata to [/tmp/RtmpNiy9q6/file21b6c059b01ff/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [/tmp/RtmpNiy9q6/file21b6c059b01ff]
> test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c059b01ff']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['/tmp/RtmpNiy9q6/file21b6c059b01ff']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 2.39 secs
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> test-io-repertoires.R: i Writing the metadata to [/tmp/RtmplVEmR8/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmplVEmR8]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 3.33 secs
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: 2.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column
> test-io-repertoires.R: v Joining plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmplVEmR8/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/tmp/RtmplVEmR8/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmplVEmR8]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 3.24 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmplVEmR8/test-no-barcodes/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/tmp/RtmplVEmR8/test-no-barcodes/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmplVEmR8/test-no-barcodes]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-no-barcodes']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-no-barcodes']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.23 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmplVEmR8/test-exclude/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/tmp/RtmplVEmR8/test-exclude/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmplVEmR8/test-exclude]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-exclude']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-exclude']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.34 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Introduced new renamed columns: v_gene
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmplVEmR8/test-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/tmp/RtmplVEmR8/test-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmplVEmR8/test-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.28 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Introduced new renamed columns: j_gene
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
> test-io-repertoires.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/tmp/RtmplVEmR8/test-exclude-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/tmp/RtmplVEmR8/test-exclude-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/tmp/RtmplVEmR8/test-exclude-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-exclude-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/tmp/RtmplVEmR8/test-exclude-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.24 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-io-repertoires.R: i Checking if all files are of the same type
> test-io-repertoires.R: v All files have the same extension
> test-io-repertoires.R:
> test-io-repertoires.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Renaming is finished
> test-io-repertoires.R:
> test-io-repertoires.R: -- Preprocessing the data
> test-io-repertoires.R: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
Saving _problems/test-io-repertoires-28.R
Saving _problems/test-io-repertoires-56.R
Saving _problems/test-io-repertoires-83.R
Saving _problems/test-io-repertoires-120.R
Saving _problems/test-io-repertoires-146.R
Saving _problems/test-io-repertoires-176.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-annotate-barcodes.R:2:3'): annotate_barcodes adds cell‑level annotations ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [78s/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.
> 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/RtmpJrmGmU/filea63cc4218d2eb/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/RtmpybVA2O/filea63e64c3acc56/annotations.parquet]
> test-annotate-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc4218d2eb/metadata.json]
> test-annotate-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc4218d2eb]
> test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc4218d2eb']
> test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc4218d2eb']
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Summary
> test-annotate-barcodes.R: i Time elapsed: 5.67 secs
Saving _problems/test-annotate-barcodes-2.R
> test-annotate-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e64c3acc56/metadata.json]
> test-annotate-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e64c3acc56]
> test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e64c3acc56']
> test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e64c3acc56']
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Summary
> test-annotate-receptors.R: i Time elapsed: 5.72 secs
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Reading repertoire data
> test-filter-barcodes.R: 1.
> test-filter-barcodes.R: /home/hornik/tmp/R.check/r-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
Saving _problems/test-annotate-receptors-2.R
> test-filter-barcodes.R: v Renaming is finished
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Preprocessing the data
> test-filter-barcodes.R: 1. exclude_columns
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1.
> test-filter-immundata-exact.R: /home/hornik/tmp/R.check/r-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: 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 [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc5c0a5552/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/RtmpybVA2O/filea63e624cf1942/annotations.parquet]
> test-filter-barcodes.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc5c0a5552/metadata.json]
> test-filter-barcodes.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc5c0a5552]
> test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc5c0a5552']
> test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-barcodes.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc5c0a5552']
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Summary
> test-filter-barcodes.R: i Time elapsed: 3.61 secs
Saving _problems/test-filter-barcodes-4.R
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Reading repertoire data
> test-filter-immundata-hamm.R: 1.
> test-filter-immundata-hamm.R: /home/hornik/tmp/R.check/r-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-exact.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e624cf1942/metadata.json]
> test-filter-immundata-exact.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e624cf1942]
> test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e624cf1942']
> test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-exact.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e624cf1942']
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Summary
> test-filter-immundata-exact.R: i Time elapsed: 3.68 secs
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Renaming the columns and schemas
> test-filter-immundata-hamm.R: v Renaming is finished
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Preprocessing the data
> test-filter-immundata-hamm.R: 1. exclude_columns
Saving _problems/test-filter-immundata-exact-2.R
> test-filter-immundata-hamm.R: 2. filter_nonproductive
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-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-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 [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc1fd6bdb8/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/RtmpybVA2O/filea63e662540b4b/annotations.parquet]
> test-filter-immundata-hamm.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc1fd6bdb8/metadata.json]
> test-filter-immundata-hamm.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc1fd6bdb8]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc1fd6bdb8']
> test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc1fd6bdb8']
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Summary
> test-filter-immundata-hamm.R: i Time elapsed: 3.63 secs
Saving _problems/test-filter-immundata-hamm-3.R
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Reading repertoire data
> test-filter-immundata-regex.R: 1.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-immundata-regex.R: 2.
> test-filter-immundata-regex.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-immundata-regex.R: i Checking if all files are of the same type
> test-filter-immundata-regex.R: v All files have the same extension
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Renaming the columns and schemas
> test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e662540b4b/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e662540b4b]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e662540b4b']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e662540b4b']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 3.66 secs
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1.
> test-filter-immundata-lev.R: /home/hornik/tmp/R.check/r-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-regex.R: 2. filter_nonproductive
> 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-lev.R:
> test-filter-immundata-lev.R: -- Renaming the columns and schemas
> 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/RtmpJrmGmU/filea63cc799e4cd8/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/RtmpybVA2O/filea63e620a0f85f/annotations.parquet]
> test-filter-immundata-regex.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc799e4cd8/metadata.json]
> test-filter-immundata-regex.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc799e4cd8]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc799e4cd8']
> test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc799e4cd8']
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Summary
> test-filter-immundata-regex.R: i Time elapsed: 3.65 secs
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-immundata-lev.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e620a0f85f/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e620a0f85f]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e620a0f85f']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e620a0f85f']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 3.69 secs
> 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
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-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
> test-filter-receptors.R: 2.
> test-filter-receptors.R: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/immundata/extdata/tsv/sample_1k_2k.tsv
> test-filter-receptors.R: i Checking if all files are of the same type
> test-filter-receptors.R: v All files have the same extension
> test-filter-immundata.R: v 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/RtmpybVA2O/filea63e639d4c110/annotations.parquet]
> test-filter-immundata.R: v Joining plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Postprocessing the data
> test-filter-immundata.R: 1. prefix_barcodes
> test-filter-receptors.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e639d4c110/metadata.json]
> test-filter-receptors.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/filea63e639d4c110]
> test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e639d4c110']
> test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-receptors.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/filea63e639d4c110']
> test-filter-receptors.R:
> test-filter-receptors.R: -- Summary
> test-filter-receptors.R: i Time elapsed: 4.15 secs
> 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/RtmpJrmGmU/filea63cc38b91939/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-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-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc38b91939/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc38b91939]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc38b91939']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc38b91939']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 5.26 secs
> 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-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: 1. exclude_columns
> test-io-repertoires.R: 2. filter_nonproductive
> test-filter-immundata.R:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-io-repertoires.R: v Preprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Aggregating the data to receptors
> test-io-repertoires.R: i No locus information found
> test-io-repertoires.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-immundata.R: 2. filter_nonproductive
> test-filter-immundata.R: v Preprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Aggregating the data to receptors
> test-filter-immundata.R: i No locus information found
> test-filter-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> test-io-repertoires.R: v Execution plan for receptor data aggregation and annotation is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Joining the metadata table with the dataset using 'filename' column
> test-filter-immundata.R: v Execution plan for receptor data aggregation and annotation is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Postprocessing the data
> test-filter-immundata.R: 1. prefix_barcodes
> test-filter-immundata.R: ! No column 'Prefix' with barcode prefixes found in the data; skipping the barcode processing
> test-filter-immundata.R: v Postprocessing plan is ready
> test-filter-immundata.R:
> test-filter-immundata.R: -- Saving the newly created ImmunData to disk
> test-filter-immundata.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc29dcf2b1/annotations.parquet]
> test-filter-immundata.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc29dcf2b1/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc29dcf2b1]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc29dcf2b1']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpJrmGmU/filea63cc29dcf2b1']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 3.93 secs
> test-io-repertoires.R: v Joining plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Postprocessing the data
> test-io-repertoires.R: 1. prefix_barcodes
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> test-io-repertoires.R: v Postprocessing plan is ready
> test-io-repertoires.R:
> test-io-repertoires.R: -- Saving the newly created ImmunData to disk
> test-io-repertoires.R: i Writing the receptor annotation data to [/home/hornik/tmp/scratch/RtmpybVA2O/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 5.39 secs
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-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/RtmpybVA2O/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 4.94 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-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/RtmpybVA2O/test-no-barcodes/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/test-no-barcodes/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/test-no-barcodes]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-no-barcodes']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-no-barcodes']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.93 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-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/RtmpybVA2O/test-exclude/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.98 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-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/RtmpybVA2O/test-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/test-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/test-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.98 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-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/RtmpybVA2O/test-exclude-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpybVA2O/test-exclude-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 1.93 secs
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1.
> test-io-repertoires.R: /home/hornik/tmp/R.check/r-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 `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.0.5
Check: tests
Result: ERROR
Running 'testthat.R' [64s]
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-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_02_04_01_50_01_15123\RtmpUNaPWK\file3b58c7d5568/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_02_04_01_50_01_15123\RtmpI3gjYm\file4864429b2b0e/annotations.parquet]
> test-annotate-barcodes.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b58c7d5568/metadata.json]
> test-annotate-barcodes.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b58c7d5568]
> test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b58c7d5568']
> test-annotate-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b58c7d5568']
> test-annotate-barcodes.R:
> test-annotate-barcodes.R: -- Summary
> test-annotate-barcodes.R: i Time elapsed: 5.48 secs
> test-annotate-receptors.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864429b2b0e/metadata.json]
Saving _problems/test-annotate-barcodes-2.R
> test-annotate-receptors.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864429b2b0e]
> test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864429b2b0e']
> test-annotate-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-annotate-receptors.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864429b2b0e']
> test-annotate-receptors.R:
> test-annotate-receptors.R: -- Summary
> test-annotate-receptors.R: i Time elapsed: 5.84 secs
> 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
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Renaming the columns and schemas
Saving _problems/test-annotate-receptors-2.R
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Reading repertoire data
> test-filter-immundata-exact.R: 1. D:\RCompile\CRANpkg\lib\4.4\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_02_04_01_50_01_15123\RtmpUNaPWK\file3b5845db2f82/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_02_04_01_50_01_15123\RtmpI3gjYm\file4864357958a8/annotations.parquet]
> test-filter-barcodes.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5845db2f82/metadata.json]
> test-filter-barcodes.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5845db2f82]
> test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5845db2f82']
> test-filter-barcodes.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-barcodes.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5845db2f82']
> test-filter-barcodes.R:
> test-filter-barcodes.R: -- Summary
> test-filter-barcodes.R: i Time elapsed: 4.7 secs
Saving _problems/test-filter-barcodes-4.R
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Reading repertoire data
> test-filter-immundata-hamm.R: 1. 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-exact.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864357958a8/metadata.json]
> test-filter-immundata-exact.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864357958a8]
> test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864357958a8']
> test-filter-immundata-exact.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-exact.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file4864357958a8']
> test-filter-immundata-exact.R:
> test-filter-immundata-exact.R: -- Summary
> test-filter-immundata-exact.R: i Time elapsed: 4.95 secs
> test-filter-immundata-hamm.R: v Renaming is finished
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Preprocessing the data
> test-filter-immundata-hamm.R: 1. exclude_columns
Saving _problems/test-filter-immundata-exact-2.R
> test-filter-immundata-hamm.R: 2. filter_nonproductive
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1. 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-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_02_04_01_50_01_15123\RtmpUNaPWK\file3b585ec76207/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_02_04_01_50_01_15123\RtmpI3gjYm\file48645a7526fd/annotations.parquet]
> test-filter-immundata-hamm.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b585ec76207/metadata.json]
> test-filter-immundata-hamm.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b585ec76207]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b585ec76207']
> test-filter-immundata-hamm.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-hamm.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b585ec76207']
> test-filter-immundata-hamm.R:
> test-filter-immundata-hamm.R: -- Summary
> test-filter-immundata-hamm.R: i Time elapsed: 5.27 secs
Saving _problems/test-filter-immundata-hamm-3.R
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Reading repertoire data
> test-filter-immundata-regex.R: 1. 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-lev.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a7526fd/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a7526fd]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a7526fd']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a7526fd']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 5.23 secs
> test-filter-immundata-regex.R: v Renaming is finished
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Preprocessing the data
> test-filter-immundata-regex.R: 1. exclude_columns
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Reading repertoire data
> test-filter-immundata-lev.R: 1. 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: 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 [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876c6aa0/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_02_04_01_50_01_15123\RtmpI3gjYm\file48645a33459a/annotations.parquet]
> test-filter-immundata-regex.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876c6aa0/metadata.json]
> test-filter-immundata-regex.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876c6aa0]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876c6aa0']
> test-filter-immundata-regex.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-regex.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876c6aa0']
> test-filter-immundata-regex.R:
> test-filter-immundata-regex.R: -- Summary
> test-filter-immundata-regex.R: i Time elapsed: 4.99 secs
Saving _problems/test-filter-immundata-regex-2.R
> test-filter-immundata-lev.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a33459a/metadata.json]
> test-filter-immundata-lev.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a33459a]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a33459a']
> test-filter-immundata-lev.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata-lev.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48645a33459a']
> test-filter-immundata-lev.R:
> test-filter-immundata-lev.R: -- Summary
> test-filter-immundata-lev.R: i Time elapsed: 5 secs
> 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
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. 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:
> test-filter-immundata.R: -- Renaming the columns and schemas
> test-filter-receptors.R:
> test-filter-receptors.R: -- Renaming the columns and schemas
> test-filter-immundata.R: v Renaming is finished
> test-filter-immundata.R:
> test-filter-immundata.R: -- Preprocessing the data
> test-filter-immundata.R: 1. exclude_columns
> test-filter-receptors.R: 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: 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-immundata.R: i Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
> 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_02_04_01_50_01_15123\RtmpI3gjYm\file48646ee5e93/annotations.parquet]
> test-filter-receptors.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48646ee5e93/metadata.json]
> test-filter-receptors.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48646ee5e93]
> test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48646ee5e93']
> test-filter-receptors.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-receptors.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\file48646ee5e93']
> test-filter-receptors.R:
> test-filter-receptors.R: -- Summary
> test-filter-receptors.R: i Time elapsed: 4.77 secs
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-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_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876612e9e/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-filter-immundata.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876612e9e/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876612e9e]
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876612e9e']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b5876612e9e']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 6.96 secs
> 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
> 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_02_04_01_50_01_15123\RtmpUNaPWK\file3b583b811e72/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-filter-immundata.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b583b811e72/metadata.json]
> test-filter-immundata.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b583b811e72]
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b583b811e72']
> test-filter-immundata.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-filter-immundata.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpUNaPWK\file3b583b811e72']
> test-filter-immundata.R:
> test-filter-immundata.R: -- Summary
> test-filter-immundata.R: i Time elapsed: 4.49 secs
> 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_02_04_01_50_01_15123\RtmpI3gjYm/annotations.parquet]
Saving _problems/test-filter-immundata-2.R
Saving _problems/test-filter-immundata-20.R
> test-io-repertoires.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 6.63 secs
> test-io-repertoires.R: Rows: 2 Columns: 4
> test-io-repertoires.R: -- Column specification --------------------------------------------------------
> test-io-repertoires.R: Delimiter: "\t"
> test-io-repertoires.R: chr (4): File, Therapy, Response, Prefix
> test-io-repertoires.R:
> test-io-repertoires.R: i Use `spec()` to retrieve the full column specification for this data.
> test-io-repertoires.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-io-repertoires.R: i Found 2/2 repertoire files from the metadata on the disk
> test-io-repertoires.R: v Metadata parsed successfully
> test-io-repertoires.R:
> test-io-repertoires.R: -- Reading repertoire data
> test-io-repertoires.R: 1. 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_02_04_01_50_01_15123\RtmpI3gjYm/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 6.82 secs
> 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_02_04_01_50_01_15123\RtmpI3gjYm\test-no-barcodes/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-no-barcodes/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-no-barcodes]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-no-barcodes']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm/test-no-barcodes']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.74 secs
> 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_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm/test-exclude']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.56 secs
> 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_02_04_01_50_01_15123\RtmpI3gjYm\test-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm/test-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.68 secs
> 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_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude-rename/annotations.parquet]
> test-io-repertoires.R: i Writing the metadata to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude-rename/metadata.json]
> test-io-repertoires.R: v ImmunData files saved to [D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude-rename]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm\test-exclude-rename']
> test-io-repertoires.R: v Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call", "j_gene") and list()]
> test-io-repertoires.R: i Reading ImmunData files from ['D:\temp\2026_02_04_01_50_01_15123\RtmpI3gjYm/test-exclude-rename']
> test-io-repertoires.R:
> test-io-repertoires.R: -- Summary
> test-io-repertoires.R: i Time elapsed: 2.73 secs
> 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 `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-annotate-receptors.R:2:3'): annotate_receptors adds receptor‑level annotations ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-barcodes.R:4:3'): filter_barcodes() filters ImmunData by a set of cell barcodes ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-exact.R:2:3'): exact matching with single and multiple patterns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-hamm.R:3:3'): Hamming fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-regex.R:2:3'): Regex matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:3:3'): Levenshtein fuzzy matching returns correct results ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata-lev.R:29:3'): combined pre-filter and fuzzy matching works correctly ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-receptors.R:3:3'): filter_receptors() filters ImmunData by a set of receptor identifiers ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:2:3'): filter() filters ImmunData by receptor-level conditions ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-filter-immundata.R:20:3'): filter() filters ImmunData by annotation-level conditions (locus) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:23:3'): read_repertoires() works with sample data and merges metadata ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:51:3'): read_repertoires() works with <metadata> ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:79:3'): read_repertoires() case 1: no barcode_col and no count_col ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:113:3'): read_repertoires() excludes specified columns ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:141:3'): read_repertoires() correctly renames columns (v_call -> v_gene) ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
── Error ('test-io-repertoires.R:168:3'): read_repertoires() excludes columns AND renames simultaneously ──
Error in `count(x$annotations)`: This operation cannot be carried out by DuckDB, and the input is a stingy duckplyr frame.
i Use `compute(prudence = "lavish")` to materialize to temporary storage and continue with duckplyr.
i See `vignette("prudence")` for other options.
Caused by error in `quo_is_null()`:
! `quo` must be a quosure
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.