Last updated on 2026-02-19 10:55:04 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.3 | 43.94 | 185.29 | 229.23 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.10.3 | 31.68 | 123.72 | 155.40 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.10.3 | 96.00 | 314.49 | 410.49 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.10.3 | 80.00 | 294.51 | 374.51 | ERROR | |
| r-devel-macos-arm64 | 0.10.3 | 12.00 | 62.00 | 74.00 | OK | |
| r-devel-windows-x86_64 | 0.10.3 | 51.00 | 187.00 | 238.00 | ERROR | |
| r-patched-linux-x86_64 | 0.10.3 | ERROR | ||||
| r-release-linux-x86_64 | 0.10.3 | 42.23 | 162.27 | 204.50 | ERROR | |
| r-release-macos-arm64 | 0.10.3 | OK | ||||
| r-release-macos-x86_64 | 0.10.3 | 31.00 | 236.00 | 267.00 | OK | |
| r-release-windows-x86_64 | 0.10.3 | 46.00 | 184.00 | 230.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.10.3 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.10.3 | 32.00 | 242.00 | 274.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.10.3 | 65.00 | 236.00 | 301.00 | ERROR |
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/RtmpYtiyjs/file33768e5b1f848/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/RtmpYtiyjs/file33768e5b1f848/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/RtmpYtiyjs/file33768e5b1f848]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYtiyjs/file33768e5b1f848']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpYtiyjs/file33768e5b1f848']
── Summary
ℹ Time elapsed: 11.48 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/RtmpiYLLnj/file30f555628972ff/annotations.parquet]
ℹ Writing the metadata to [/tmp/RtmpiYLLnj/file30f555628972ff/metadata.json]
✔ ImmunData files saved to [/tmp/RtmpiYLLnj/file30f555628972ff]
ℹ Reading ImmunData files from ['/tmp/RtmpiYLLnj/file30f555628972ff']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/RtmpiYLLnj/file30f555628972ff']
── Summary
ℹ Time elapsed: 3.99 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:
> ### 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. /data/gannet/ripley/R/test-clang/immundata/extdata/tsv/sample_0_1k.tsv
2. /data/gannet/ripley/R/test-clang/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/RtmpItGGEb/working_dir/Rtmpiw8iuP/file2b455e1e8ea8e0/annotations.parquet]
ℹ Writing the metadata to [/tmp/RtmpItGGEb/working_dir/Rtmpiw8iuP/file2b455e1e8ea8e0/metadata.json]
✔ ImmunData files saved to [/tmp/RtmpItGGEb/working_dir/Rtmpiw8iuP/file2b455e1e8ea8e0]
ℹ Reading ImmunData files from ['/tmp/RtmpItGGEb/working_dir/Rtmpiw8iuP/file2b455e1e8ea8e0']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/RtmpItGGEb/working_dir/Rtmpiw8iuP/file2b455e1e8ea8e0']
── Summary
ℹ Time elapsed: 56.88 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-fedora-clang
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. /data/gannet/ripley/R/test-dev/immundata/extdata/tsv/sample_0_1k.tsv
2. /data/gannet/ripley/R/test-dev/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/RtmpOlrbVF/working_dir/RtmpJiIYix/file33502d6e6fa606/annotations.parquet]
ℹ Writing the metadata to [/tmp/RtmpOlrbVF/working_dir/RtmpJiIYix/file33502d6e6fa606/metadata.json]
✔ ImmunData files saved to [/tmp/RtmpOlrbVF/working_dir/RtmpJiIYix/file33502d6e6fa606]
ℹ Reading ImmunData files from ['/tmp/RtmpOlrbVF/working_dir/RtmpJiIYix/file33502d6e6fa606']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/RtmpOlrbVF/working_dir/RtmpJiIYix/file33502d6e6fa606']
── Summary
ℹ Time elapsed: 29.01 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-fedora-gcc
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_0_1k.tsv
2. D:\RCompile\CRANpkg\lib\4.6\immundata\extdata\tsv\sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [D:\temp\2026_02_17_01_50_00_13006\RtmpOGjUEU\filec27c6817433b/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_17_01_50_00_13006\RtmpOGjUEU\filec27c6817433b/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_17_01_50_00_13006\RtmpOGjUEU\filec27c6817433b]
ℹ Reading ImmunData files from ['D:\temp\2026_02_17_01_50_00_13006\RtmpOGjUEU\filec27c6817433b']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_17_01_50_00_13006\RtmpOGjUEU\filec27c6817433b']
── Summary
ℹ Time elapsed: 4.84 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-windows-x86_64
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/RtmpFWBX72/file2e53ab66eb5f74/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/RtmpFWBX72/file2e53ab66eb5f74/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/RtmpFWBX72/file2e53ab66eb5f74]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpFWBX72/file2e53ab66eb5f74']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/RtmpFWBX72/file2e53ab66eb5f74']
── Summary
ℹ Time elapsed: 6.75 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: 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-release-gcc/Work/build/Packages/immundata/extdata/tsv/sample_0_1k.tsv
2.
/home/hornik/tmp/R.check/r-release-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/Rtmpk8moZN/file3495fe69b1a79c/annotations.parquet]
ℹ Writing the metadata to [/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c/metadata.json]
✔ ImmunData files saved to [/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/home/hornik/tmp/scratch/Rtmpk8moZN/file3495fe69b1a79c']
── Summary
ℹ Time elapsed: 5.61 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-release-linux-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:
> ### Name: airr_public
> ### Title: Public indices - pairwise repertoire overlap
> ### Aliases: airr_public airr_public_intersection airr_public_jaccard
>
> ### ** Examples
>
> # Limit the number of threads used by the underlying DB for this session.
> # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
> db_exec("SET threads TO 1")
> # Load data
> immdata <- get_test_idata() |> agg_repertoires("Therapy")
Rows: 2 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): File, Therapy, Response, Prefix
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
ℹ Found 2/2 repertoire files from the metadata on the disk
✔ Metadata parsed successfully
── Reading repertoire data
1. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_0_1k.tsv
2. D:\RCompile\CRANpkg\lib\4.5\immundata\extdata\tsv\sample_1k_2k.tsv
ℹ Checking if all files are of the same type
✔ All files have the same extension
── Renaming the columns and schemas
✔ Renaming is finished
── Preprocessing the data
1. exclude_columns
2. filter_nonproductive
✔ Preprocessing plan is ready
── Aggregating the data to receptors
ℹ No locus information found
ℹ Processing data as immune repertoire tables - no counts, no barcodes, no chain pairing possible
✔ Execution plan for receptor data aggregation and annotation is ready
── Joining the metadata table with the dataset using 'filename' column
✔ Joining plan is ready
── Postprocessing the data
1. prefix_barcodes
✔ Postprocessing plan is ready
── Saving the newly created ImmunData to disk
ℹ Writing the receptor annotation data to [D:\temp\2026_02_15_01_50_00_5770\RtmpwZ2lov\file18430462b6101/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_15_01_50_00_5770\RtmpwZ2lov\file18430462b6101/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_15_01_50_00_5770\RtmpwZ2lov\file18430462b6101]
ℹ Reading ImmunData files from ['D:\temp\2026_02_15_01_50_00_5770\RtmpwZ2lov\file18430462b6101']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_15_01_50_00_5770\RtmpwZ2lov\file18430462b6101']
── Summary
ℹ Time elapsed: 5.01 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-release-windows-x86_64
Version: 0.10.3
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
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_16_01_50_00_25772\RtmpUFNHza\file55543948534/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_16_01_50_00_25772\RtmpUFNHza\file55543948534/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_16_01_50_00_25772\RtmpUFNHza\file55543948534]
ℹ Reading ImmunData files from ['D:\temp\2026_02_16_01_50_00_25772\RtmpUFNHza\file55543948534']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_16_01_50_00_25772\RtmpUFNHza\file55543948534']
── Summary
ℹ Time elapsed: 6.87 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