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### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ELMER.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ELMER_2.20.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ELMER/DESCRIPTION' ... OK
* this is package 'ELMER' version '2.20.0'
* 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
* 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 ... WARNING
Missing or unexported object: 'TCGAbiolinks::GDCquery_Maf'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TCGA.pipe: warning in render_report(genome = genome, mode = mode, title
  = paste0(disease, " report"), minSubgroupFrac = ifelse(mode ==
  "supervised", 1, 0.2), mae = mae.path, direction = direction,
  group.col = group.col, group1 = group1, group2 = group2, dir.out =
  results.path, out_file = file.path(results.path, paste0(disease,
  "_report.html"))): partial argument match of 'mae' to 'mae.file'
Stat.nonpara: no visible global function definition for 'head'
Stat.nonpara: no visible global function definition for 'tail'
Stat.nonpara.permu: no visible global function definition for 'head'
Stat.nonpara.permu: no visible global function definition for 'tail'
TFsurvival.plot: no visible global function definition for 'head'
TFsurvival.plot: no visible global function definition for 'tail'
addMutCol: no visible binding for global variable 'Hugo_Symbol'
calcDistNearestTSS: no visible binding for global variable
  'DistanceTSS'
get.top.tf.by.pval: no visible global function definition for 'head'
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 head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'render_report':
render_report
  Code: function(title = "Report", mae.file, group.col, group1, group2,
                 direction, dir.out, genome = "hg38", mode =
                 "supervised", minSubgroupFrac = 0.2, minMetdiff = 0.3,
                 metfdr = 0.01, permu = 10000, rawpval = 0.01, pe =
                 0.01, nprobes = 10, lower.OR = 1.1, out_file =
                 file.path(getwd(), "report.html"), funcivar = FALSE)
  Docs: function(title = "Report", mae.file, group.col, group1, group2,
                 direction, dir.out, genome = "hg38", mode =
                 "supervised", minSubgroupFrac = "20%", minMetdiff =
                 "0.3", metfdr = "0.01", permu = "10000", rawpval =
                 "0.01", pe = "0.01", nprobes = "10", lower.OR = "1.1",
                 out_file = file.path(getwd(), "report.html"), funcivar
                 = FALSE)
  Mismatches in argument default values:
    Name: 'minSubgroupFrac' Code: 0.2 Docs: "20%"

* 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                    94.81   2.58  128.73
createMAE                    25.83   2.03   40.07
getRandomPairs               24.93   0.95   26.62
schematic.plot               21.93   0.33   25.01
get.enriched.motif           18.42   0.67   20.54
scatter.plot                 14.82   0.12   14.95
get.feature.probe             9.81   0.57   11.00
GetNearGenes                  9.56   0.13   10.83
get.pair                      9.11   0.08    9.17
preAssociationProbeFiltering  6.89   0.49    7.70
getRegionNearGenes            7.00   0.36    7.36
getTCGA                       2.13   0.11    5.58
* 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: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/ELMER.Rcheck/00check.log'
for details.