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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ELMER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ELMER_2.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ELMER.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.30.0’
* 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 ‘ELMER’ 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 code 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
addMutCol: no visible binding for global variable 'Hugo_Symbol'
calcDistNearestTSS: no visible binding for global variable
  'DistanceTSS'
getRegionNearGenes : f: no visible binding for global variable 'Side'
getRegionNearGenes: no visible binding for global variable 'ID'
getTFtargets: no visible binding for global variable 'TF'
Undefined global functions or variables:
  DistanceTSS Hugo_Symbol ID Side TF
* checking Rd files ... NOTE
checkRd: (-1) createBigWigDNAmetArray.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{track.names}{Provide a  list of track names (.bw) otherwise the deault is the will be {samples}.bw}
       |                                                                                             ^
* 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
TCGA.pipe                    151.379  4.059 178.011
schematic.plot                46.203  3.417  59.316
getRandomPairs                43.247  1.350  50.176
createMAE                     40.335  3.707  80.108
get.enriched.motif            29.736  3.461  38.095
scatter.plot                  31.622  0.823  36.421
get.feature.probe             19.452  0.861  22.453
get.pair                      18.111  0.384  20.253
GetNearGenes                  16.930  0.446  19.697
preAssociationProbeFiltering  13.159  1.501  25.482
getRegionNearGenes            12.100  0.416  24.802
get.permu                      8.124  0.335   9.468
getTCGA                        5.154  0.371  17.096
get.TFs                        4.533  0.782   5.785
TF.rank.plot                   4.626  0.142   5.365
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ELMER.Rcheck/00check.log’
for details.