• using R version 4.5.2 Patched (2026-01-31 r89374)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘immunarch/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘immunarch’ version ‘0.10.3’
• package encoding: UTF-8
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• checking for sufficient/correct file permissions ... OK
• checking whether package ‘immunarch’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
• checking package directory ... OK
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• checking examples ... [10s/16s] 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
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• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [4s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR