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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.12.0’
* 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 ‘CAGEr’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
paraclu                    125.836  0.882 136.373
exportToTrack              105.286  0.840 112.849
aggregateTagClusters        58.212  0.535  62.209
scoreShift                  44.729  0.586  47.709
quantilePositions           36.309  0.237  38.226
annotateCTSS                35.596  0.340  38.120
distclu                     26.991  0.205  28.419
plotExpressionProfiles      19.917  0.243  21.290
getExpressionProfiles       15.220  0.122  16.216
CustomConsensusClusters     13.528  0.104  14.204
CAGEexp-class                9.040  1.387  10.797
cumulativeCTSSdistribution   9.721  0.096  10.298
TSSlogo                      6.953  0.107   7.666
consensusClustersDESeq2      6.048  0.042   6.414
plotReverseCumulatives       5.834  0.064   6.181
plotAnnot                    5.739  0.076   6.099
mergeCAGEsets                5.595  0.063   5.847
getShiftingPromoters         5.531  0.041   5.825
expressionClasses            5.429  0.036   5.699
plotInterquantileWidth       5.050  0.042   5.457
* 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: OK