##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELMER.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ELMER_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ELMER.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ELMER/DESCRIPTION' ... OK
* this is package 'ELMER' version '2.16.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
TCGA.pipe                    85.36   2.45   92.78
getRandomPairs               29.31   1.28   30.53
createMAE                    27.28   0.31   35.00
get.enriched.motif           22.98   0.79   26.42
schematic.plot               22.84   0.17   26.86
scatter.plot                 15.06   0.03   15.10
get.feature.probe            11.13   0.56   11.69
preAssociationProbeFiltering 10.79   0.24   11.01
GetNearGenes                  9.85   0.32   10.25
get.pair                      9.51   0.10    9.61
getRegionNearGenes            6.87   0.42    7.30
getTCGA                       2.39   0.05    6.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
TCGA.pipe                    83.74   0.77   87.19
getRandomPairs               24.33   0.66   24.93
createMAE                    23.25   0.41   23.66
schematic.plot               22.67   0.23   26.58
get.enriched.motif           19.87   0.70   23.32
scatter.plot                 16.30   0.03   16.33
get.pair                     10.56   0.16   10.69
GetNearGenes                  9.84   0.12    9.96
get.feature.probe             9.63   0.31    9.93
preAssociationProbeFiltering  7.94   0.18    8.11
getRegionNearGenes            8.00   0.09    8.10
getTCGA                       2.69   0.06    6.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ELMER.Rcheck/00check.log'
for details.