* using log directory ‘/srv/hornik/tmp/CRAN/TOmicsVis.Rcheck’
* using R Under development (unstable) (2023-07-19 r84711)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (3)
    GNU Fortran (Debian 12.3.0-5) 12.3.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘TOmicsVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TOmicsVis’ version ‘1.2.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/9s] NOTE
Maintainer: ‘Benben Miao <benben.miao@outlook.com>’

Found the following (possibly) invalid URLs:
  URL: https://cloud.r-project.org/web/packages/TOmicsVis/
    From: inst/doc/Tutorials.html
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/TOmicsVis/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  The canonical URL of the CRAN page for a package is 
    https://CRAN.R-project.org/package=pkgname
  Canonical CRAN.R-project.org URLs use https.
* 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 ‘TOmicsVis’ can be installed ... [21s/21s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘README.Rmd’
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [26s/26s] 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 ... [0s/0s] 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 ... [23s/23s] ERROR
Running examples in ‘TOmicsVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gene_cluster_trend
> ### Title: Gene cluster trend plot for visualizing gene expression trend
> ###   profile in multiple samples.
> ### Aliases: gene_cluster_trend
> 
> ### ** Examples
> 
> # 1. Library TOmicsVis package
> library(TOmicsVis)
> 
> # 2. Use example dataset gene_cluster_data
> data(gene_cluster_data)
> head(gene_cluster_data)
           Time1      Time2       Time3
Gene1  0.1774993  1.6563226 -1.15259948
Gene2 -0.5037254 -0.5207024  0.46416071
Gene3  0.1050310  0.6079246  0.72893247
Gene4 -1.1791537  0.4340085  0.41061745
Gene5  0.8368975 -0.7047414 -1.46114720
Gene6  0.2611762  0.1351524 -0.01890809
> 
> # 3. Default parameters
> gene_cluster_trend(gene_cluster_data)
Error in exprs(eset) : could not find function "exprs"
Calls: gene_cluster_trend -> <Anonymous> -> logical
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [19s/19s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tutorials.Rmd’ using rmarkdown

Quitting from lines 521-532 [gene_cluster_trend] (Tutorials.Rmd)
Error: processing vignette ‘Tutorials.Rmd’ failed with diagnostics:
could not find function "exprs"
--- failed re-building ‘Tutorials.Rmd’

SUMMARY: processing the following file failed:
  ‘Tutorials.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs