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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_2.24.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ELMER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.24.1’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'GDCquery(project = paste0("TCGA-", ': unused argument (legacy = TRUE) 
  Note: possible error in 'GDCquery(project = paste0("TCGA-", ': unused arguments (file.type = "normalized_results", legacy = TRUE) 
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ELMER.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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'
get450K: possible error in GDCquery(project = paste0("TCGA-",
  toupper(disease)), data.category = "DNA methylation", legacy = TRUE,
  platform = "Illumina Human Methylation 450"): unused argument (legacy
  = TRUE)
getRNAseq: possible error in GDCquery(project = paste0("TCGA-",
  toupper(disease)), data.category = "Gene expression", data.type =
  "Gene expression quantification", platform = "Illumina HiSeq",
  file.type = "normalized_results", experimental.strategy = "RNA-Seq",
  legacy = TRUE): unused arguments (file.type = "normalized_results",
  legacy = TRUE)
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 ... 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                    85.285  2.181 133.759
getRandomPairs               30.397  0.845  48.344
createMAE                    28.267  1.612  53.413
schematic.plot               24.815  0.500  51.502
get.enriched.motif           19.487  0.884  31.842
scatter.plot                 16.624  0.250  25.638
get.feature.probe            14.351  0.425  23.003
get.pair                     11.251  0.182  17.457
GetNearGenes                 10.043  0.208  15.230
preAssociationProbeFiltering  9.180  0.367  15.064
getRegionNearGenes            8.631  0.291  13.523
get.permu                     4.228  0.155   6.711
getTCGA                       2.172  0.096  22.670
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ELMER.Rcheck/00check.log’
for details.