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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomicInstability.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomicInstability_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/genomicInstability.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomicInstability/DESCRIPTION’ ... OK
* this is package ‘genomicInstability’ version ‘1.0.0’
* 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 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 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> : <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 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", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘genomicInstability-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomicInstabilityScore
> ### Title: Genomic Instability Analysis
> ### Aliases: genomicInstabilityScore
> 
> ### ** Examples
> 
> 
> eh <- ExperimentHub::ExperimentHub()
snapshotDate(): 2021-10-19
> dset <- eh[["EH5419"]]
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing package(s) 'GSE103322'
Error in UseMethod("conditionMessage") : 
  no applicable method for 'conditionMessage' applied to an object of class "character"
Calls: [[ ... tryCatchList -> tryCatchOne -> doTryCatch -> download.file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/genomicInstability.Rcheck/00check.log’
for details.