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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GenomicPlot_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicPlot.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 16.299  4.646  20.009
plot_region                13.725  5.086  13.882
plot_locus                 14.215  3.974  15.274
plot_5parts_metagene       11.289  5.284  14.006
plot_locus_with_random     10.275  3.517  11.261
plot_start_end             10.745  2.624  13.097
plot_peak_annotation        7.285  0.476   7.761
get_targeted_genes          5.989  0.059   6.049
get_txdb_features           5.274  0.110   5.384
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicPlot.Rcheck/00check.log’
for details.