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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings ELMER_2.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ELMER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.26.0’
* 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 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
TCGA.pipe                    94.144  2.418  98.221
getRandomPairs               30.842  1.947  38.399
schematic.plot               27.179  1.819  48.142
createMAE                    25.496  2.653  38.741
get.enriched.motif           20.391  1.149  24.640
scatter.plot                 17.950  0.635  18.625
get.feature.probe            12.604  1.211  16.814
get.pair                     11.667  0.566  12.256
GetNearGenes                 11.593  0.172  11.790
preAssociationProbeFiltering 10.316  0.918  14.099
getRegionNearGenes            8.856  0.199   9.075
getTCGA                       2.831  0.295  24.203
* 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 ...
  ‘analysis_data_input.Rmd’ using ‘UTF-8’... OK
  ‘analysis_diff_meth.Rmd’ using ‘UTF-8’... OK
  ‘analysis_get_pair.Rmd’ using ‘UTF-8’... OK
  ‘analysis_gui.Rmd’ using ‘UTF-8’... OK
  ‘analysis_motif_enrichment.Rmd’ using ‘UTF-8’... OK
  ‘analysis_regulatory_tf.Rmd’ using ‘UTF-8’... OK
  ‘index.Rmd’ using ‘UTF-8’... OK
  ‘input.Rmd’ using ‘UTF-8’... OK
  ‘pipe.Rmd’ using ‘UTF-8’... OK
  ‘plots_TF.Rmd’ using ‘UTF-8’... OK
  ‘plots_heatmap.Rmd’ using ‘UTF-8’... OK
  ‘plots_motif_enrichment.Rmd’ using ‘UTF-8’... OK
  ‘plots_scatter.Rmd’ using ‘UTF-8’... OK
  ‘plots_schematic.Rmd’ using ‘UTF-8’... OK
  ‘usecase.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ELMER.Rcheck/00check.log’
for details.