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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MethCP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MethCP_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MethCP.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MethCP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethCP’ version ‘1.14.0’
* 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 ‘MethCP’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'DMLtest(o, group1, group2, ': unused argument (BPPARAM = bpparam()) 
  Warning: Package 'MethCP' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.17-bioc/meat/MethCP.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
* 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 startup messages can be suppressed ... 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 ... NOTE
calcLociStat : <anonymous>: possible error in DMLtest(o, group1,
  group2, equal.disp = FALSE, smoothing = FALSE, BPPARAM = bpparam()):
  unused argument (BPPARAM = bpparam())
createBsseqObject: no visible binding for global variable ‘plogis’
createBsseqObject: no visible global function definition for
  ‘combineList’
Undefined global functions or variables:
  combineList plogis
Consider adding
  importFrom("stats", "plogis")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
calcLociStatTimeCourse 7.935  2.705   2.149
calcLociStat           4.027  0.140   7.663
* 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:
      rowMedians
  
  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-MethCP.R:20:5'): methylKit ───────────────────────────────────
  `... <- NULL` did not produce any messages.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  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 ...
  ‘methcp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘methcp.Rmd’ using rmarkdown
Error: processing vignette 'methcp.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘methcp.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MethCP.Rcheck/00check.log’
for details.