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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SOMNiBUS.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SOMNiBUS_1.8.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/SOMNiBUS.Rcheck'
* using R version 4.3.0 RC (2023-04-13 r84269 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SOMNiBUS/DESCRIPTION' ... OK
* this is package 'SOMNiBUS' version '1.8.0'
* 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 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 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
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     207.59   7.46  215.10
runSOMNiBUS           172.91   6.32  179.30
binomRegMethModelPlot  31.07   2.61   33.70
binomRegMethModelPred  31.28   1.80   33.09
binomRegMethPredPlot   31.29   1.78   33.08
splitDataByGene        12.17   2.10   14.36
splitDataByChromatin    9.00   0.30    9.35
formatFromBismark       3.54   0.08   16.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SOMNiBUS
###
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* installing to library 'F:/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 version 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 1.8.0 
NOTE: - Logging level is set to INFO 
      - Output file is F:\biocbuild\bbs-3.17-bioc\tmpdir\Rtmpaw5kie/somnibus.log 
      - See 'package?SOMNiBUS' for help.
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-42. 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")