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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SOMNiBUS_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SOMNiBUS.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SOMNiBUS/DESCRIPTION’ ... OK
* this is package ‘SOMNiBUS’ version ‘1.7.0’
* 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 ‘SOMNiBUS’ 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 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
testStat: no visible global function definition for ‘pf’
Undefined global functions or variables:
  pf
Consider adding
  importFrom("stats", "pf")
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 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
binomRegMethModel     445.953  2.075 448.051
runSOMNiBUS           363.776  1.732 365.520
binomRegMethModelPlot  50.332  0.180  50.514
binomRegMethModelPred  48.761  0.176  48.939
binomRegMethPredPlot   48.743  0.168  48.912
splitDataByGene        14.392  0.608  15.047
splitDataByChromatin   12.224  0.748  16.809
formatFromBismark       4.869  0.220   5.037
* 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:
      intersect, setdiff, setequal, union
  
  > 
  > test_check("SOMNiBUS")
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 243 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_runSOMNiBUS.R:84'): Test incorrect values while calling partitioning functions ──
  `runSOMNiBUS(...)` did not throw an error.
  ── Failure ('test_splitDataByGene.R:125'): Test incorrect values ───────────────
  `splitDataByGene(...)` did not throw an error.
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 243 ]
  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 ...
  ‘SOMNiBUS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SOMNiBUS.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SOMNiBUS
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SOMNiBUS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SOMNiBUS)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SOMNiBUS)
Package SOMNiBUS version 1.7.0 
NOTE: - Logging level is set to INFO 
      - Output file is /tmp/RtmpSyUydT/somnibus.log 
      - See 'package?SOMNiBUS' for help.
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-41. For overview type 'help("mgcv-package")'.
> library(dplyr)

Attaching package: 'dplyr'

The following object is masked from 'package:nlme':

    collapse

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("SOMNiBUS")
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 243 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_runSOMNiBUS.R:84'): Test incorrect values while calling partitioning functions ──
`runSOMNiBUS(...)` did not throw an error.
── Failure ('test_splitDataByGene.R:125'): Test incorrect values ───────────────
`splitDataByGene(...)` did not throw an error.

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 243 ]
Error: Test failures
Execution halted