##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:XhybCasneuf.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings XhybCasneuf_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/XhybCasneuf.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘XhybCasneuf/DESCRIPTION’ ... OK
* this is package ‘XhybCasneuf’ version ‘1.45.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘XhybCasneuf’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘affy’ ‘ath1121501cdf’ ‘grid’ ‘methods’ ‘tinesath1cdf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runSimulation : ourmedianpolish: no visible global function definition
  for ‘medpolish’
runSimulation: no visible global function definition for ‘hsv’
runSimulation: no visible global function definition for ‘rnorm’
runSimulation: no visible global function definition for ‘layout’
runSimulation: no visible global function definition for ‘par’
runSimulation: no visible global function definition for ‘matplot’
runSimulation: no visible binding for global variable
  ‘generateExprVal.method.mas’
runSimulation: no visible binding for global variable
  ‘generateExprVal.method.liwong’
runSimulation: no visible global function definition for ‘legend’
runSimulation: no visible global function definition for ‘cor’
plotExample,XhybExamples: no visible global function definition for
  ‘par’
plotExample,XhybExamples: no visible global function definition for
  ‘brewer.pal’
plotExample,XhybExamples: no visible global function definition for
  ‘matplot’
plotExample,XhybExamples: no visible global function definition for
  ‘lines’
plotExample,XhybExamples: no visible global function definition for
  ‘legend’
plotExample,XhybExamples : <anonymous>: no visible global function
  definition for ‘cor’
plotExample,XhybExamples: no visible global function definition for
  ‘abline’
Undefined global functions or variables:
  abline brewer.pal cor generateExprVal.method.liwong
  generateExprVal.method.mas hsv layout legend lines matplot medpolish
  par rnorm
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "matplot", "par")
  importFrom("stats", "cor", "medpolish", "rnorm")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) AffysTissue.Rd:21: Escaped LaTeX specials: \_
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  AffysTissue.noBl.rda      202Kb    154Kb       xz
  AffysTissue.rda           741Kb    491Kb       xz
  AffysTissueMC.rda         886Kb    589Kb       xz
  CustomsTissue.noBl.rda    153Kb    120Kb       xz
  CustomsTissue.rda         552Kb    373Kb       xz
  CustomsTissueMC.rda       688Kb    468Kb       xz
* 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
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/XhybCasneuf.Rcheck/00check.log’
for details.