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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:genomicInstability.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings genomicInstability_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/genomicInstability.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 ‘genomicInstability/DESCRIPTION’ ... OK
* this is package ‘genomicInstability’ version ‘1.13.0’
* package encoding: UTF-8
* 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 ‘genomicInstability’ 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
mixGaussianFit : <anonymous>: warning in normalmixEM(x, lambda =
  param$lambda, mu = param$m, sd = param$sigma, epsilon = 1e-50):
  partial argument match of 'sd' to 'sd.constr'
aecdf1: no visible global function definition for ‘quantile’
aecdf1: no visible global function definition for ‘ecdf’
aecdf1: no visible binding for global variable ‘tl2’
aecdf1: no visible binding for global variable ‘iq2’
aecdf1: no visible global function definition for ‘epd’
aecdf1: no visible global function definition for ‘lm’
aecdf1: no visible global function definition for ‘predict’
aecdf1: no visible global function definition for ‘qnorm’
colorScale: no visible global function definition for ‘col2rgb’
colorScale : <anonymous>: no visible global function definition for
  ‘rgb’
generateChromosomeGeneSet: no visible global function definition for
  ‘data’
generateChromosomeGeneSet: no visible binding for global variable
  ‘hg38’
generateChromosomeGeneSet: no visible binding for global variable
  ‘mm10’
generateChromosomeGeneSet: no visible binding for global variable
  ‘genePosition’
getPeaks: no visible global function definition for ‘density’
getPeaks3: no visible global function definition for ‘density’
getPeaks3: no visible global function definition for ‘smooth.spline’
getPeaks3: no visible global function definition for ‘predict’
getPeaks3 : <anonymous>: no visible global function definition for
  ‘approx’
giDensityPlot: no visible global function definition for ‘density’
giDensityPlot: no visible global function definition for ‘lines’
giLikelihood: no visible global function definition for ‘sd’
giLikelihood: no visible global function definition for ‘predict’
mixGaussianFit : <anonymous>: no visible global function definition for
  ‘capture.output’
mixGaussianFit : <anonymous> : <anonymous>: no visible global function
  definition for ‘dnorm’
mixGaussianFit: no visible global function definition for ‘density’
plot.inferCNV: no visible global function definition for ‘pdf’
plot.inferCNV: no visible global function definition for ‘png’
plot.inferCNV: no visible global function definition for ‘jpeg’
plot.inferCNV: no visible global function definition for ‘layout’
plot.inferCNV: no visible global function definition for ‘par’
plot.inferCNV: no visible global function definition for ‘axis’
plot.inferCNV: no visible global function definition for ‘dev.off’
plot.mgfit: no visible global function definition for ‘rainbow’
plot.mgfit: no visible global function definition for ‘density’
plot.mgfit: no visible global function definition for ‘dnorm’
plot.mgfit: no visible global function definition for ‘axis’
plot.mgfit: no visible global function definition for ‘polygon’
plot.mgfit: no visible global function definition for ‘lines’
plothm: no visible global function definition for ‘par’
plothm: no visible global function definition for ‘layout’
plothm: no visible global function definition for ‘axis’
plothm: no visible global function definition for ‘image’
plothm.: no visible global function definition for ‘image’
predict.mgfit : <anonymous>: no visible global function definition for
  ‘dnorm’
sREA: no visible global function definition for ‘qnorm’
sortRowsByHclust: no visible global function definition for ‘dist’
sortRowsByHclust: no visible global function definition for ‘hclust’
Undefined global functions or variables:
  approx axis capture.output col2rgb data density dev.off dist dnorm
  ecdf epd genePosition hclust hg38 image iq2 jpeg layout lines lm mm10
  par pdf png polygon predict qnorm quantile rainbow rgb sd
  smooth.spline tl2
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
             "rainbow", "rgb")
  importFrom("graphics", "axis", "image", "layout", "lines", "par",
             "polygon")
  importFrom("stats", "approx", "density", "dist", "dnorm", "ecdf",
             "hclust", "lm", "predict", "qnorm", "quantile", "sd",
             "smooth.spline")
  importFrom("utils", "capture.output", "data")
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 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
genomicInstabilityScore 29.217  1.565  31.078
giDensityPlot           23.904  1.873  26.039
giLikelihood            23.567  1.944  25.741
plot.inferCNV           23.297  1.786  25.358
inferCNV                22.243  1.863  24.336
* 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-3.21-bioc/meat/genomicInstability.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL genomicInstability
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘genomicInstability’ ...
** 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 (genomicInstability)