* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PRECAST.Rcheck’
* using R Under development (unstable) (2025-12-14 r89168)
* 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 ‘PRECAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PRECAST’ version ‘1.8’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] 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 ‘PRECAST’ can be installed ... [66s/66s] OK
* used C++ compiler: ‘Debian clang version 21.1.6 (3)’
* 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/9s] 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 ... [8s/8s] OK
* checking whether startup messages can be suppressed ... [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 ... [38s/38s] 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 ... [9s/9s] 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 ... [11s/11s] ERROR
Running examples in ‘PRECAST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IntegrateSpaData
> ### Title: Integrate multiple SRT data
> ### Aliases: IntegrateSpaData
> 
> ### ** Examples
> 
>   data(PRECASTObj)
>   PRECASTObj <- SelectModel(PRECASTObj)
>   seuInt <- IntegrateSpaData(PRECASTObj, species='unknown')
Using only PRECAST results to obtain the batch corrected gene expressions since species is unknown or the genelist in PRECASTObj has less than 5 overlapp with the housekeeping genes of given species.
Start integration...
2025-12-15 09:07:47.65478 : ***** Data integration finished!, 0 mins elapsed.
Put the data into a new Seurat object...
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. └─PRECAST::IntegrateSpaData(PRECASTObj, species = "unknown")
 2.   ├─SeuratObject::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 ... [15s/15s] 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