* using log directory 'd:/Rcompile/CRANpkg/local/4.6/immunarch.Rcheck'
* using R Under development (unstable) (2026-02-13 r89414 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-02-14 07:40:21 UTC
* checking for file 'immunarch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunarch' version '0.10.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'immunarch' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s] OK
* checking loading without being on the library search path ... [4s] OK
* checking whether startup messages can be suppressed ... [4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [24s] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [10s] 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_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80/annotations.parquet]
ℹ Writing the metadata to [D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80/metadata.json]
✔ ImmunData files saved to [D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80]
ℹ Reading ImmunData files from ['D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80']
✔ Loaded ImmunData with the receptor schema: [c("cdr3_aa", "v_call") and list()]
ℹ Reading ImmunData files from ['D:\temp\2026_02_14_01_50_00_18536\RtmpQpspT7\file17d4c2e074c80']

── Summary 
ℹ Time elapsed: 4.73 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [5s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... [23s] OK
* DONE
Status: 1 ERROR