* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CAESAR.Suite.Rcheck’
* using R Under development (unstable) (2025-12-22 r89217)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.6 (2)
    Debian flang version 21.1.6 (2)
* running under: Debian GNU/Linux forky/sid
* 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 ... [3s/4s] 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 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 ‘CAESAR.Suite’ can be installed ... [49s/49s] OK
* used C++ compiler: ‘Debian clang version 21.1.7 (1)’
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [37s/37s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] ERROR
Running examples in ‘CAESAR.Suite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotation_mat
> ### Title: Annotate Cells Using Distance Matrix and Marker Frequencies
> ### Aliases: annotation_mat
> 
> ### ** Examples
> 
> data(toydata)
> 
> seu <- toydata$seu
> markers <- toydata$markers
> 
> seu <- ProFAST::pdistance(seu, reduction = "caesar")
Calculate co-embedding distance...
> distce <- Seurat::GetAssayData(object = seu, slot = "data", assay = "distce")
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. ├─Seurat::GetAssayData(object = seu, slot = "data", assay = "distce")
 2. └─SeuratObject:::GetAssayData.Seurat(...)
 3.   └─SeuratObject::.Deprecate(...)
 4.     └─lifecycle::deprecate_stop(...)
 5.       └─lifecycle:::deprecate_stop0(msg)
 6.         └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [20s/20s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR