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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagene2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metagene2_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metagene2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘metagene2/DESCRIPTION’ ... OK
* this is package ‘metagene2’ version ‘1.16.0’
* 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 ‘metagene2’ 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 R 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 ... OK
* checking Rd files ... WARNING
checkRd: (5) Bam_Handler.Rd:20: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:40: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:44: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:48: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:52: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:56: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:59-60: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:69-70: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:451: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:456: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:461: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:466: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:475: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:480: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:485: \item in \describe must have non-empty label
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plot_metagene 5.618  0.023   5.643
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘metagene2.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/metagene2.Rcheck/00check.log’
for details.