Last updated on 2026-03-11 01:53:30 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.3 | 45.78 | 186.25 | 232.03 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.10.3 | 29.21 | 193.06 | 222.27 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.10.3 | 87.00 | 451.52 | 538.52 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.10.3 | 86.00 | 298.75 | 384.75 | ERROR | |
| r-devel-macos-arm64 | 0.10.3 | 12.00 | 62.00 | 74.00 | OK | |
| r-devel-windows-x86_64 | 0.10.3 | 53.00 | 194.00 | 247.00 | ERROR | |
| r-patched-linux-x86_64 | 0.10.3 | 43.70 | 162.96 | 206.66 | ERROR | |
| r-release-linux-x86_64 | 0.10.3 | 41.77 | 163.24 | 205.01 | 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 | 48.00 | 184.00 | 232.00 | 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 | 64.00 | 239.00 | 303.00 | 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/Rtmp6nCGEd/filede0b6353e9a9/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-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:
> ### 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/Rtmpg3txi4/working_dir/Rtmp04L8zS/file568cb58b739af/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-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_03_07_01_50_00_12595\RtmpM9l1cJ\file11df05e48a79/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.10.3
Check: examples
Result: ERROR
Running examples in ‘immunarch-Ex.R’ failed
The error most likely occurred in:
> 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/RtmpataYMv/file249a054d6620fd/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-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/Rtmp4iLcLK/filebb26738ea93c4/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-release-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_03_06_11_10_10_4045\RtmpKMUbZQ\file37f862ff5a2f/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.10.3
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
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_03_09_01_50_00_19831\RtmpoJ2iCo\fileda2045a81d88/annotations.parquet]
Error in `duckfun()`:
! {"exception_type":"Binder","exception_message":"Invalid named parameter \"compression_level\" for function read_parquet\nCandidates:\n binary_as_string BOOLEAN\n can_have_nan BOOLEAN\n compression VARCHAR\n debug_use_openssl BOOLEAN\n encryption_config ANY\n explicit_cardinality UBIGINT\n file_row_number BOOLEAN\n filename ANY\n hive_partitioning BOOLEAN\n hive_types ANY\n hive_types_autocast BOOLEAN\n parquet_version VARCHAR\n schema ANY\n union_by_name BOOLEAN\n"}
Backtrace:
▆
1. ├─immundata::agg_repertoires(get_test_idata(), "Therapy")
2. │ └─checkmate::assert_r6(idata, "ImmunData")
3. │ └─checkmate::checkR6(...)
4. ├─immundata::get_test_idata()
5. │ └─immundata:::get_test_idata_tsv_with_metadata()
6. │ └─immundata::read_repertoires(...)
7. │ └─immundata::write_immundata(idata, output_folder)
8. │ ├─duckplyr::compute_parquet(...)
9. │ └─duckplyr:::compute_parquet.duckplyr_df(...)
10. │ └─duckplyr::read_parquet_duckdb(path, prudence = prudence, options = read_options)
11. │ └─duckplyr::read_file_duckdb(...)
12. │ └─duckplyr:::duckfun(...)
13. │ └─duckdb$rel_from_table_function(...)
14. │ └─duckdb:::rethrow_rapi_rel_from_table_function(...)
15. │ ├─rlang::try_fetch(...)
16. │ │ ├─base::tryCatch(...)
17. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. │ │ └─base::withCallingHandlers(...)
21. │ └─duckdb:::rapi_rel_from_table_function(...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))
24. └─handlers[[1L]](cnd)
25. └─duckdb:::rethrow_error_from_rapi(e, call)
26. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-oldrel-windows-x86_64
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