##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicPlot_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘1.4.0’
* 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 ‘GenomicPlot’ 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 ... NOTE
get_targeted_genes: no visible binding for global variable ‘5'UTR’
get_targeted_genes: no visible binding for global variable ‘3'UTR’
handle_bam: no visible global function definition for ‘seqlevelsStyle’
handle_bam: no visible global function definition for
  ‘seqlevelsStyle<-’
handle_bed: no visible global function definition for ‘seqlevelsStyle’
handle_bed: no visible global function definition for
  ‘seqlevelsStyle<-’
handle_bedGraph: no visible global function definition for
  ‘seqlevelsStyle’
handle_bedGraph: no visible global function definition for
  ‘seqlevelsStyle<-’
handle_bw: no visible global function definition for ‘seqlevelsStyle’
handle_bw: no visible global function definition for ‘seqlevelsStyle<-’
plot_bam_correlation: no visible binding for global variable ‘.’
plot_peak_annotation: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . 3'UTR 5'UTR seqlevelsStyle seqlevelsStyle<-
* 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 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
plot_start_end_with_random 18.404  8.674  21.795
plot_region                13.996  7.119  14.126
plot_locus                 12.786  4.789  13.309
plot_5parts_metagene       10.875  5.911  11.953
plot_start_end             11.113  3.370  12.481
plot_locus_with_random      9.309  4.126  10.116
plot_peak_annotation        7.561  0.100   7.666
get_targeted_genes          6.510  0.074   6.590
get_txdb_features           5.857  0.049   5.909
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-plotFunctions.R’
  Running ‘test-shortFunctions.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck/00check.log’
for details.