* using log directory 'd:/RCompile/CRANincoming/R-devel/CAESAR.Suite.Rcheck'
* using R Under development (unstable) (2025-12-17 r89193 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
* checking for file 'CAESAR.Suite/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAESAR.Suite' version '0.3.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [12s] OK
* 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 'CAESAR.Suite' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [17s] OK
* checking whether the package can be loaded with stated dependencies ... [17s] OK
* checking whether the package can be unloaded cleanly ... [16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s] OK
* checking whether the namespace can be unloaded cleanly ... [17s] OK
* checking loading without being on the library search path ... [18s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'SeuratObject'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [79s] OK
* checking Rd files ... 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [24s] ERROR
Running examples in 'CAESAR.Suite-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CAESAR.RUV
> ### Title: Perform Batch Correction and Integration with CAESAR Using
> ###   Housekeeping Genes
> ### Aliases: CAESAR.RUV
> 
> ### ** Examples
> 
> data(toydata)
> 
> seu <- toydata$seu
> markers <- toydata$markers
> 
> seu <- ProFAST::pdistance(seu, reduction = "caesar")
Calculate co-embedding distance...
> 
> marker.freq <- markerList2mat(list(markers))
> anno_res <- CAESAR.annotation(seu, marker.freq, cal.confidence = FALSE, cal.proportions = FALSE)
> 
> seuList <- list(seu, seu)
> distList <- list(anno_res$ave.dist, anno_res$ave.dist)
> seuInt <- CAESAR.RUV(seuList, distList, species = "human", verbose = TRUE)
Using both housekeeping genes and CAESAR results for batch correction.
Error:
! The `slot` argument of `SetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─CAESAR.Suite::CAESAR.RUV(...)
 2.   ├─Seurat::SetAssayData(...)
 3.   └─SeuratObject:::SetAssayData.Seurat(...)
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [24s] OK
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING