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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GSEAmining.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GSEAmining_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GSEAmining.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘GSEAmining/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEAmining’ version ‘1.9.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSEAmining’ 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 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 ... OK
* checking Rd files ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GSEAmining-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clust_group_cores
> ### Title: clust_group_cores
> ### Aliases: clust_group_cores
> 
> ### ** Examples
> 
> data(genesets_sel)
> gs.cl <- gm_clust(genesets_sel)
Error in loadNamespace(x) : there is no package called ‘tm’
Calls: gm_clust ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-gm_clust.R:10:3'): Test that gm_clust produces an hclust object ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'tm'
  Backtrace:
      ▆
   1. ├─GSEAmining::gm_clust(gs.filt) at test-gm_clust.R:10:2
   2. │ └─tidytext::cast_dtm(...)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GSEAmining.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘GSEAmining.Rmd’ using rmarkdown
Quitting from lines 164-166 (GSEAmining.Rmd) 
Error: processing vignette 'GSEAmining.Rmd' failed with diagnostics:
there is no package called 'tm'
--- failed re-building ‘GSEAmining.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GSEAmining.Rcheck/00check.log’
for details.