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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recoup_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/recoup.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recoup/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘recoup’ version ‘1.33.0’
* 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 ‘recoup’ 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 code 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
Unexported objects imported by ':::' calls:
  ‘biomaRt:::.generateFilterXML’ ‘biomaRt:::.setResultColNames’
  ‘biomaRt:::martCheck’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘biomaRt:::martVSchema’ ‘txdbmaker:::GFF_FEATURE_TYPES’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘makeHorizontalAnnotation’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readBamIntervals: no visible binding for global variable ‘bam.file’
recoupCorrelation: no visible binding for global variable ‘Index’
recoupCorrelation: no visible binding for global variable ‘Coverage’
recoupCorrelation: no visible binding for global variable ‘Condition’
recoupCorrelation: no visible binding for global variable ‘Design’
recoupHeatmap : <anonymous>: no visible global function definition for
  ‘grid.text’
recoupProfile: no visible binding for global variable ‘Signal’
recoupProfile: no visible binding for global variable ‘Condition’
recoupProfile: no visible binding for global variable ‘Design’
Undefined global functions or variables:
  Condition Coverage Design Index Signal bam.file grid.text
* checking Rd files ... NOTE
checkRd: (-1) recoup.Rd:210-211: Lost braces
   210 |     \code{region}{Minimum flank is 0bp and maximum is
       |                  ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
mergeRuns             46.809 10.681  47.481
profileMatrix         24.497  9.065  24.511
recoupPlot            18.969  5.353  18.657
recoup                18.773  5.430  18.378
kmeansDesign          17.957  4.513  18.718
sliceObj              17.495  4.930  17.323
simpleGetSet          16.603  4.618  15.414
recoupProfile         10.706  1.621  13.409
recoupCorrelation      9.739  1.431  11.183
recoupHeatmap          9.266  1.379  10.586
coverageRef            7.966  0.138   8.290
buildCustomAnnotation  5.580  0.274   7.676
calcCoverage           5.069  0.061   5.352
getAnnotation          3.010  0.149   8.705
preprocessRanges       0.410  0.045  21.390
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/recoup.Rcheck/00check.log’
for details.