* using log directory ‘/srv/hornik/tmp/CRAN_pretest/numbat.Rcheck’
* using R Under development (unstable) (2026-02-03 r89375)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-04 04:22:33 UTC
* checking for file ‘numbat/DESCRIPTION’ ... OK
* this is package ‘numbat’ version ‘1.5.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Teng Gao <tgaoteng@gmail.com>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  CNV (2:24)
  CNVs (7:73, 7:279)
  Gao (7:881)
  al (7:888)
  et (7:885)
  microenvironment (7:493)
  scRNA (2:42, 7:89, 7:690)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2026-01-30 as requires archived package
    'pryr'.
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘numbat’ can be installed ... [21s/21s] OK
* used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] 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 ... [14s/14s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [4s/4s] ERROR
Running examples in ‘numbat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect_clonal_loh
> ### Title: Call clonal LOH using SNP density.  Rcommended for cell lines or
> ###   tumor samples with no normal cells.
> ### Aliases: detect_clonal_loh
> 
> ### ** Examples
> 
> segs_loh = detect_clonal_loh(bulk_example)
Error in `summarise()`:
ℹ In argument: `Y_obs = unique(na.omit(Y_obs))`.
ℹ In group 1: `CHROM = 5`, `gene = ""`, `gene_start = NA`, `gene_end = NA`.
Caused by error:
! `Y_obs` must be size 1, not 0.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─numbat::detect_clonal_loh(bulk_example)
  2. │ └─... %>% mutate(gene_length = gene_end - gene_start)
  3. ├─dplyr::mutate(., gene_length = gene_end - gene_start)
  4. ├─dplyr::summarise(...)
  5. ├─dplyr:::summarise.grouped_df(...)
  6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  7. │   └─base::withCallingHandlers(...)
  8. ├─dplyr:::dplyr_internal_error(...)
  9. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 10. │   └─rlang:::signal_abort(cnd, .file)
 11. │     └─base::signalCondition(cnd)
 12. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 13.   └─dplyr (local) handler(cnd)
 14.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [3s/3s] OK
  Running ‘testthat.R’ [2s/2s]
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [3s/3s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE