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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicPlot_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GenomicPlot.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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      23.477  7.339  27.050
plot_region                     18.623  6.591  18.047
plot_locus                      18.182  4.192  18.658
plot_5parts_metagene            14.264  5.322  15.627
plot_locus_with_random          13.677  4.135  14.294
plot_start_end                  14.542  2.572  16.382
plot_peak_annotation            10.416  0.179  10.629
get_targeted_genes               8.836  0.124   8.979
get_txdb_features                7.630  0.075   7.721
prepare_5parts_genomic_features  6.341  0.047   6.409
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-plotFunctions.R’