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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_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.10.0’
* 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 ... NOTE
checkRd: (-1) inputFiles.Rd:28: Lost braces
    28 | code{\link{CAGEexp}} objects.
       |     ^
checkRd: (-1) inputFilesType.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:53-55: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
S3 methods shown with full name in Rd file 'rowsum.RleDataFrame.Rd':
  'rowsum.RleDataFrame'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
clusterCTSS                89.095  0.695 105.946
exportToTrack              86.998  0.686 102.271
aggregateTagClusters       71.418  1.517  87.718
scoreShift                 58.103  0.936  69.906
quantilePositions          53.661  0.957  66.140
annotateCTSS               52.799  0.894  63.798
cumulativeCTSSdistribution 45.171  1.306  54.727
CustomConsensusClusters    25.006  0.755  31.076
getExpressionProfiles      24.854  0.394  29.280
plotExpressionProfiles     23.416  0.479  28.671
CAGEexp-class               8.852  1.312  12.289
expressionClasses          10.020  0.091  11.821
consensusClustersDESeq2     9.429  0.163  11.177
getShiftingPromoters        8.830  0.145  10.408
distclu-functions           6.719  0.395   8.405
plotAnnot                   5.835  0.074   7.337
mergeCAGEsets               5.549  0.087   6.846
plotInterquantileWidth      4.906  0.122   6.065
CAGEr_Multicore             4.215  0.036   5.453
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘CAGEr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CAGEr)