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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:DmelSGI.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings DmelSGI_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/DmelSGI.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DmelSGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DmelSGI’ version ‘1.20.0’
* 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 ‘DmelSGI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 139.3Mb
  sub-directories of 1Mb or more:
    Rscripts    1.7Mb
    data      137.3Mb
* 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
callInteractions: no visible global function definition for ‘p.adjust’
fitMatrices: no visible global function definition for ‘png’
fitMatrices: no visible global function definition for ‘dev.off’
makeDall: no visible global function definition for ‘mad’
mymedpolish: no visible binding for global variable ‘median’
mymedpolish : <anonymous>: no visible binding for global variable
  ‘median’
mymedpolish: no visible global function definition for ‘median’
orderDim: no visible global function definition for ‘cor’
orderDim: no visible global function definition for ‘hclust’
orderDim: no visible global function definition for ‘as.dist’
orderSpiderAxis: no visible global function definition for ‘dist’
plot2Phenotypes: no visible global function definition for ‘layout’
plot2Phenotypes: no visible global function definition for ‘par’
plot2Phenotypes: no visible global function definition for ‘points’
plot2Phenotypes: no visible global function definition for ‘arrows’
plot2Phenotypes: no visible global function definition for ‘segments’
plot2Phenotypes: no visible global function definition for ‘abline’
plot2Phenotypes: no visible global function definition for ‘text’
plotHairballLabels: no visible global function definition for ‘text’
plotHairballLabels: no visible global function definition for ‘lines’
plotPIdata: no visible global function definition for ‘par’
plotPIdata: no visible global function definition for ‘abline’
saveHeatmapFile: no visible global function definition for ‘png’
saveHeatmapFile: no visible global function definition for ‘dev.off’
saveHeatmapFile: no visible global function definition for ‘cairo_pdf’
selectByStability: no visible global function definition for ‘lm’
selectByStability : <anonymous>: no visible global function definition
  for ‘cor’
subSampleForStabilitySelectionFct : <anonymous>: no visible global
  function definition for ‘median’
subSampleForStabilitySelectionFct : <anonymous>: no visible global
  function definition for ‘mad’
Undefined global functions or variables:
  abline arrows as.dist cairo_pdf cor dev.off dist hclust layout lines
  lm mad median p.adjust par png points segments text
Consider adding
  importFrom("grDevices", "cairo_pdf", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "layout", "lines", "par",
             "points", "segments", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "lm", "mad",
             "median", "p.adjust")
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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/DmelSGI.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL DmelSGI
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘DmelSGI’ ...
** using staged installation
** R
** data
** inst
** 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 (DmelSGI)