* using log directory 'd:/Rcompile/CRANpkg/local/4.2/SMDIC.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* checking for file 'SMDIC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SMDIC' version '0.1.4'
* 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 'SMDIC' 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 R 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 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 ... [42s] 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [19s] ERROR
Running examples in 'SMDIC-Ex.R' failed
The error most likely occurred in:

> ### Name: exp2cell
> ### Title: exp2cell
> ### Aliases: exp2cell
> 
> ### ** Examples
> 
> #get breast cancer gene expression profile.
> exp.example<-GetExampleData("exp.example")
> 
> #perform the exp2cell method. Method must be one of "xCell","ssGSEA" and "CIBERSORT".
> cellmatrix<-exp2cell(exp=exp.example,method="ssGSEA") #cell abundance matrix
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [18s] ERROR
Error(s) in re-building vignettes:
--- re-building 'SMDIC.Rmd' using rmarkdown

Quitting from lines 63-70 [unnamed-chunk-2] (SMDIC.Rmd)
Error: processing vignette 'SMDIC.Rmd' failed with diagnostics:
useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
--- failed re-building 'SMDIC.Rmd'

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs