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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RnaSeqSampleSize_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RnaSeqSampleSize.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnaSeqSampleSize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RnaSeqSampleSize’ version ‘2.13.0’
* 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 ‘RnaSeqSampleSize’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
analyze_dataset: no visible binding for global variable ‘logFC’
analyze_dataset: no visible binding for global variable
  ‘DispersionInTreatmentVsControl’
analyze_dataset: no visible binding for global variable
  ‘DispersionInControlOnly’
plot_gene_counts_range: no visible binding for global variable ‘name’
plot_gene_counts_range: no visible binding for global variable ‘value’
plot_mappedReads_percent: no visible binding for global variable
  ‘Reads’
plot_mappedReads_percent: no visible binding for global variable
  ‘Category’
plot_mappedReads_percent: no visible binding for global variable
  ‘Tissue’
plot_mappedReads_percent: no visible binding for global variable
  ‘MappedReadsPercent’
Undefined global functions or variables:
  Category DispersionInControlOnly DispersionInTreatmentVsControl
  MappedReadsPercent Reads Tissue logFC name value
* checking Rd files ... NOTE
checkRd: (-1) plot_power_curve.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{las}{Numeric in {0,1,2,3}; the style of axis labels.}
       |                       ^
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
est_power_curve          10.374  0.467  10.986
sample_size_distribution  6.907  0.306   7.288
optimize_parameter        6.094  0.246   6.402
convertIdOneToOne         1.244  0.168   8.839
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.19-bioc/meat/RnaSeqSampleSize.Rcheck/00check.log’
for details.