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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:betaHMM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings betaHMM_1.3.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/betaHMM.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘betaHMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘betaHMM’ version ‘1.3.1’
* 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 ‘betaHMM’ 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 ...Warning: program compiled against libxml 212 using older 211
 OK
* checking code 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot                   1.443  0.081  43.739
betaHMM                1.253  0.110  26.448
betaHMMResults         1.025  0.100  24.727
packageHelpers         0.763  0.051  22.366
dmr_identification     0.752  0.059  25.811
betaHMMrun             0.709  0.093  22.872
dmr_identification_run 0.747  0.050  23.888
dmc_identification_run 0.737  0.059  23.880
dmrResults             0.753  0.036  24.346
summary                0.722  0.051  23.022
dmc_identification     0.721  0.012  23.714
dmcResults             0.681  0.017  22.794
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R/bin/BATCH: line 60: 1776335 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  The following object is masked from 'package:stats4':
  
      plot
  
  The following object is masked from 'package:graphics':
  
      plot
  
  The following object is masked from 'package:base':
  
      plot
  
  > 
  > test_check("betaHMM")
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette without corresponding tangle output:
  ‘betaHMM.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ...