##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChromHeatMap.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChromHeatMap_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChromHeatMap.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘ChromHeatMap/DESCRIPTION’ ... OK
* this is package ‘ChromHeatMap’ version ‘1.60.0’
* 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 ‘ChromHeatMap’ 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
createChrMatrix: no visible global function definition for ‘new’
makeRangedDataList : .makeGRanges: no visible global function
  definition for ‘as’
plotChrMap: no visible global function definition for ‘new’
makeChrStrandData,matrix: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  as new
Consider adding
  importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) ALLs.chr22.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ALLs.chr22.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cytobands.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cytobands.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cytobands.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cytobands.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cytobands.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cytobands.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stains.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stains.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stains.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stains.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stains.Rd:26-28: Lost braces in \itemize; meant \describe ?
* 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
makeRangedDataList 3.275  0.149   9.976
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ChromHeatMap.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ChromHeatMap
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ChromHeatMap’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChromHeatMap)