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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RUVnormalize.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RUVnormalize_1.40.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RUVnormalize.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RUVnormalize/DESCRIPTION’ ... OK
* this is package ‘RUVnormalize’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘spams’
* 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 ‘RUVnormalize’ 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 ... NOTE
'library' or 'require' call to ‘spams’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterativeRUV: no visible global function definition for ‘kmeans’
myPalette: no visible global function definition for ‘col2rgb’
myPalette: no visible global function definition for ‘rgb’
svdPlot: no visible global function definition for ‘pdf’
svdPlot: no visible global function definition for ‘par’
svdPlot: no visible global function definition for ‘points’
svdPlot: no visible global function definition for ‘text’
svdPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  col2rgb dev.off kmeans par pdf points rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
  importFrom("graphics", "par", "points", "text")
  importFrom("stats", "kmeans")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RUVnormalize.Rcheck/00check.log’
for details.