* using log directory 'd:/Rcompile/CRANpkg/local/4.5/MSiP.Rcheck'
* using R version 4.5.2 (2025-10-31 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 'MSiP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSiP' version '1.3.7'
* 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 'MSiP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... [4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s] OK
* checking whether the package can be unloaded cleanly ... [4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s] OK
* checking whether the namespace can be unloaded cleanly ... [5s] OK
* checking loading without being on the library search path ... [5s] 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 ... [11s] 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 ... [1s] 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 ... [5s] ERROR
Running examples in 'MSiP-Ex.R' failed
The error most likely occurred in:

> ### Name: Weighted.matrixModel
> ### Title: Weighted.matrixModel
> ### Aliases: Weighted.matrixModel
> 
> ### ** Examples
> 
> data(SampleDatInput)
> datScoring <- Weighted.matrixModel(SampleDatInput)
Error:
! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `across()` instead.
Backtrace:
     ▆
  1. ├─MSiP::Weighted.matrixModel(SampleDatInput)
  2. │ └─... %>% dplyr::select(-1)
  3. ├─dplyr::select(., -1)
  4. ├─base (local) set_rownames(., .$Experiment.id)
  5. │ └─base::is.data.frame(x)
  6. ├─base::as.data.frame(.)
  7. └─dplyr::summarise_each(., funs(max(.)))
  8.   └─dplyr:::each_defunct("summarise_each()")
  9.     └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()")
 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 ... [6s] ERROR
Error(s) in re-building vignettes:
--- re-building 'MSiP_tutorial.Rmd' using knitr

Quitting from MSiP_tutorial.Rmd:45-49 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `across()` instead.
---
Backtrace:
    ▆
 1. ├─MSiP::diceCoefficient(SampleDatInput)
 2. │ ├─base::suppressWarnings(...)
 3. │ │ └─base::withCallingHandlers(...)
 4. │ └─... %>% dplyr::select(-1)
 5. ├─dplyr::select(., -1)
 6. └─dplyr::summarise_each(., funs(max(.)))
 7.   └─dplyr:::each_defunct("summarise_each()")
 8.     └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()")
 9.       └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MSiP_tutorial.Rmd' failed with diagnostics:
`summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `across()` instead.
--- failed re-building 'MSiP_tutorial.Rmd'

SUMMARY: processing the following file failed:
  'MSiP_tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 2 ERRORs