* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SMDIC.Rcheck’
* using R Under development (unstable) (2024-10-14 r87233)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘SMDIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMDIC’ version ‘0.1.6’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Junwei Han <hanjunwei1981@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Baotong",
                      family = "Zheng",
                      role = "aut"),
               person(given = "Junwei",
                      family = "Han",
                      role = c("aut", "cre"),
                      email = "hanjunwei1981@163.com"))
as necessary.
* 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 ‘SMDIC’ can be installed ... [25s/25s] 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [34s/34s] OK
* checking Rd files ... [0s/0s] 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 ... [3s/3s] 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 ... [9s/9s] ERROR
Running examples in ‘SMDIC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
ℹ GSVA version 1.53.27
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection': unable to find an inherited method for function ‘GeneSet’ for signature ‘type = "factor"’
Calls: exp2cell ... GeneSetCollection -> mapply -> <Anonymous> -> GeneSet -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8s/8s] 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:
error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection': unable to find an inherited method for function 'GeneSet' for signature 'type = "factor"'
--- 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 ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE