* using log directory 'd:/RCompile/CRANincoming/R-devel/ProFAST.Rcheck'
* using R Under development (unstable) (2025-12-13 r89166 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 'ProFAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ProFAST' version '1.7'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... 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 'ProFAST' 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 ... [15s] OK
* checking whether the package can be loaded with stated dependencies ... [11s] OK
* checking whether the package can be unloaded cleanly ... [10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s] OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... [14s] 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 ... [43s] 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 ... [19s] ERROR
Running examples in 'ProFAST-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find.signature.genes
> ### Title: Find the signature genes for each group of cell/spots
> ### Aliases: find.signature.genes
> 
> ### ** Examples
> 
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp

Attaching package: 'SeuratObject'

The following objects are masked from 'package:base':

    intersect, t

> data(pbmc3k_subset)
> pbmc3k_subset <- pdistance(pbmc3k_subset, reduction='ncfm')
Calculate co-embedding distance...
> df_list_rna <- find.signature.genes(pbmc3k_subset)
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. └─ProFAST::find.signature.genes(pbmc3k_subset)
  2.   └─pbapply::pblapply(...)
  3.     └─base::lapply(X, FUN, ...)
  4.       └─ProFAST (local) FUN(X[[i]], ...)
  5.         └─ProFAST:::gene.activity.score.seu(...)
  6.           ├─SeuratObject::GetAssayData(seu, assay = assay, slot = "data")
  7.           └─SeuratObject:::GetAssayData.Seurat(seu, assay = assay, slot = "data")
  8.             └─SeuratObject::.Deprecate(...)
  9.               └─lifecycle::deprecate_stop(...)
 10.                 └─lifecycle:::deprecate_stop0(msg)
 11.                   └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR