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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicPlot.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomicPlot_1.3.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicPlot/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicPlot' version '1.3.1'
* 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 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      14.61   0.86  267.72
plot_start_end                   9.79   0.53  133.25
plot_peak_annotation             9.57   0.33   10.10
get_targeted_genes               8.68   0.59    9.63
plot_5parts_metagene             8.38   0.79  214.55
plot_locus                       8.70   0.32   94.47
get_txdb_features                7.50   0.24    8.01
plot_locus_with_random           6.26   0.43   95.64
plot_region                      6.39   0.28  132.11
prepare_5parts_genomic_features  5.17   0.22    5.62
plot_bam_correlation             1.14   0.15   25.20
effective_size                   0.64   0.10   27.25
parallel_countOverlaps           0.36   0.12   25.47
parallel_scoreMatrixBin          0.31   0.05   21.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-plotFunctions.R'