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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.26.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘1.26.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
  inst/extdata/.batchtools.conf.R
  inst/extdata/.batchtools.conf.R.sge
  inst/extdata/.batchtools.conf.R.torque
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.change_branch: no visible binding for global variable ‘.’
.cmdToCwl: no visible binding for global variable ‘slash_line’
.find_long_branch: no visible binding for global variable ‘.’
.parse_step : <anonymous>: no visible binding for global variable ‘.’
.parse_step: no visible binding for global variable ‘.’
GOHyperGAll_Subset: no visible binding for global variable
  ‘test_sample’
GOHyperGAll_Subset: no visible binding for global variable ‘GO_CC_DF’
SPRdata: no visible global function definition for ‘SimpleList’
appendParam: no visible binding for global variable ‘commandline’
countRangeset: no visible global function definition for ‘import.bed’
countRangeset: no visible global function definition for
  ‘summarizeOverlaps’
featureCoverage: no visible global function definition for ‘Rle’
featuretypeCounts: no visible global function definition for ‘first’
genFeatures: no visible global function definition for ‘seqlengths<-’
goBarplot: no visible binding for global variable ‘SampleMatch’
goBarplot: no visible binding for global variable ‘Sample’
loadWF: no visible global function definition for ‘metadata’
loadWorkflow: no visible global function definition for ‘metadata’
olRanges: no visible global function definition for ‘seqlengths<-’
olRanges: no visible global function definition for ‘seqlengths’
olRanges: no visible global function definition for ‘Rle’
renameParam: no visible binding for global variable ‘commandline’
replaceParam: no visible binding for global variable ‘commandline’
replaceParam: no visible binding for global variable ‘replacing’
subsetParam: no visible binding for global variable ‘commandline’
subsetRmd: no visible binding for global variable ‘.’
addAssay,SummarizedExperiment: no visible global function definition
  for ‘SimpleList’
addMetadata,SummarizedExperiment: no visible global function definition
  for ‘metadata’
Undefined global functions or variables:
  . GO_CC_DF Rle Sample SampleMatch SimpleList commandline first
  import.bed metadata replacing seqlengths seqlengths<- slash_line
  summarizeOverlaps test_sample
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
genFeatures 21.779  0.426  22.217
run_DESeq2  19.934  0.048  19.983
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.