Last updated on 2026-02-04 02:51:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.3 | 43.95 | 282.30 | 326.25 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.10.3 | 29.66 | 123.39 | 153.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.10.3 | 88.00 | 430.19 | 518.19 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.10.3 | 82.00 | 417.80 | 499.80 | OK | |
| r-devel-windows-x86_64 | 0.10.3 | 48.00 | 278.00 | 326.00 | OK | |
| r-patched-linux-x86_64 | 0.10.3 | 43.48 | 250.58 | 294.06 | OK | |
| r-release-linux-x86_64 | 0.10.3 | 42.85 | 247.69 | 290.54 | OK | |
| 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 | 270.00 | 318.00 | OK | |
| 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 | 66.00 | 361.00 | 427.00 | OK |
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/Rtmp8L9Hj5/file133c4f5ee32b80/annotations.parquet]
ℹ Writing the metadata to [/tmp/Rtmp8L9Hj5/file133c4f5ee32b80/metadata.json]
✔ ImmunData files saved to [/tmp/Rtmp8L9Hj5/file133c4f5ee32b80]
ℹ Reading ImmunData files from ['/tmp/Rtmp8L9Hj5/file133c4f5ee32b80']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['/tmp/Rtmp8L9Hj5/file133c4f5ee32b80']
── Summary
ℹ Time elapsed: 3.68 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: 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