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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ELMER_2.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ELMER.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.31.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 loading without being on the library search path ... 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                    75.420  1.406  83.994
createMAE                    22.381  1.061  24.359
getRandomPairs               22.787  0.634  23.821
schematic.plot               20.203  0.625  29.487
get.pair                     19.573  0.267  22.118
get.enriched.motif           16.968  0.466  20.435
scatter.plot                 12.191  0.353  12.547
get.feature.probe            10.921  0.504  12.843
preAssociationProbeFiltering  8.575  0.869   9.748
GetNearGenes                  8.059  0.228   8.289
get.permu                     6.047  0.033   6.493
getRegionNearGenes            5.644  0.059   5.703
TF.rank.plot                  4.712  0.148   7.049
getTCGA                       2.608  0.308  14.118
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ELMER.Rcheck/00check.log’
for details.