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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SOMNiBUS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* 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 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 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     281.210  5.238 502.640
runSOMNiBUS           231.323  6.267 425.932
binomRegMethModelPlot  29.837  0.744  53.695
binomRegMethPredPlot   29.720  0.581  53.702
binomRegMethModelPred  29.429  0.659  51.098
splitDataByGene        15.669  2.899  33.362
splitDataByChromatin   10.426  0.540  20.992
formatFromBismark       4.053  0.295   7.908
splitDataByDensity      3.135  0.051   5.730
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SOMNiBUS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 /tmp/RtmpnJrfVB/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")
2023-10-19 03:01:32.432 R[10999:45093410] XType: com.apple.fonts is not accessible.
2023-10-19 03:01:32.438 R[10999:45093410] XType: XTFontStaticRegistry is enabled.