* using log directory 'd:/Rcompile/CRANpkg/local/4.4/CACIMAR.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'CACIMAR/DESCRIPTION' ... OK
* this is package 'CACIMAR' version '1.0.0'
* package encoding: UTF-8
* 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 'CACIMAR' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... [9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s] OK
* checking whether the package can be unloaded cleanly ... [10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s] OK
* checking whether the namespace can be unloaded cleanly ... [10s] OK
* checking loading without being on the library search path ... [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 ... [25s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 ... [4s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [14s] ERROR
Running examples in 'CACIMAR-Ex.R' failed
The error most likely occurred in:

> ### Name: Format_Markers_Frac
> ### Title: Format marker genes for plotting
> ### Aliases: Format_Markers_Frac
> 
> ### ** Examples
> 
> data("pbmc_small")
> all.markers <- Identify_Markers(pbmc_small)
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
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. └─CACIMAR::Identify_Markers(pbmc_small)
  2.   └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
  3.     └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
  4.       └─CACIMAR:::Markertest(...)
  5.         ├─Seurat::GetAssayData(object = object, slot = "data")
  6.         └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
  7.           └─SeuratObject::.Deprecate(...)
  8.             └─lifecycle::deprecate_stop(...)
  9.               └─lifecycle:::deprecate_stop0(msg)
 10.                 └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [18s] ERROR
  Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(CACIMAR)
  Loading required package: Seurat
  Loading required package: SeuratObject
  Loading required package: sp
  
  Attaching package: 'SeuratObject'
  
  The following objects are masked from 'package:base':
  
      intersect, t
  
  > 
  > test_check("CACIMAR")
  
  mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN 
      14207     37432     10353      3238       273       128 
  [1] "mm_zf_0T1"
  [1] "mm_zf_1T0"
  [1] "mm_zf_1T1"
  [1] "mm_zf_1TN"
  [1] "mm_zf_NT1"
  [1] "mm_zf_NTN"
  Using NCS as value column: use value.var to override.
  Calculating cluster 0
  Calculating cluster 1
  Calculating cluster 2
  [1] "0"
  Saving _problems/test-test1-10.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  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. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
    2.   └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
    3.     └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
    4.       └─CACIMAR:::Markertest(...)
    5.         ├─Seurat::GetAssayData(object = object, slot = "data")
    6.         └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
    7.           └─SeuratObject::.Deprecate(...)
    8.             └─lifecycle::deprecate_stop(...)
    9.               └─lifecycle:::deprecate_stop0(msg)
   10.                 └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 2 ERRORs