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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RegEnrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RegEnrich_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RegEnrich.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 ‘RegEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegEnrich’ version ‘1.10.0’
* 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 ‘RegEnrich’ 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
.local_grNet: no visible global function definition for ‘is’
.plotRegTarExpr: no visible global function definition for ‘is’
.rankScore: no visible global function definition for ‘as’
.regSEA: no visible global function definition for ‘new’
DEA: no visible global function definition for ‘is’
DEA_LRT_LM: no visible global function definition for ‘is’
RegenrichSet: no visible global function definition for ‘as’
RegenrichSet: no visible global function definition for ‘new’
getParamsIn: no visible global function definition for ‘is’
getResultsNames: no visible global function definition for ‘is’
head.Score: no visible global function definition for ‘S3Part’
newDeaSet: no visible global function definition for ‘new’
newEnrich: no visible global function definition for ‘new’
newScore: no visible global function definition for ‘new’
newTopNetwork: no visible global function definition for ‘new’
print.Score: no visible global function definition for ‘S3Part’
tail.Score: no visible global function definition for ‘S3Part’
head,Score: no visible global function definition for ‘S3Part’
regSEA,TopNetwork: no visible global function definition for ‘new’
show,Score: no visible global function definition for ‘S3Part’
tail,Score: no visible global function definition for ‘S3Part’
Undefined global functions or variables:
  S3Part as is new
Consider adding
  importFrom("methods", "S3Part", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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_Enrich    17.526  0.618  24.200
plotRegTarExpr 10.620  0.193  16.691
RegenrichSet    3.246  0.036   5.041
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RegEnrich.Rcheck/00check.log’
for details.