* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/Platypus.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘Platypus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Platypus’ version ‘3.6.0’
* 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 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 ‘Platypus’ can be installed ... [30s/30s] OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [51s/51s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
* checking examples with --run-donttest ... ERROR
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 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 ... OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/Platypus.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:21.54, 178.18 + 22.00