BioC experimental data: CHECK report for HD2013SGI on malbec2

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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HD2013SGI_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/HD2013SGI.Rcheck’
* using R version 3.4.1 (2017年06月30日)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HD2013SGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HD2013SGI’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
 ‘RColorBrewer’ ‘gplots’ ‘geneplotter’ ‘splots’ ‘limma’ ‘vcd’ ‘LSD’
 ‘EBImage’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘HD2013SGI’ can be installed ... OK
* checking installed package size ... NOTE
 installed size is 526.7Mb
 sub-directories of 1Mb or more:
 data 524.1Mb
 doc 1.4Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
 ‘EBImage’ ‘LSD’ ‘RColorBrewer’ ‘geneplotter’ ‘gplots’ ‘limma’
 ‘splots’ ‘vcd’
 These packages need to be imported from (in the NAMESPACE file)
 for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
 almost never needs to use ::: for its own objects:
 ‘humanReadableNames’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for ‘unit’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘pushViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘viewport’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘grid.layout’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘grid.rect’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘grid.raster’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘popViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
 ‘grid.text’
HD2013SGIHeatmapHuman: no visible global function definition for ‘gpar’
HD2013SGImaineffects: no visible binding for global variable ‘median’
HD2013SGImaineffects : <anonymous>: no visible binding for global
 variable ‘median’
HD2013SGImaineffects: no visible global function definition for
 ‘median’
HD2013SGIorderDim: no visible global function definition for ‘cor’
HD2013SGIorderDim: no visible global function definition for ‘hclust’
HD2013SGIorderDim: no visible global function definition for ‘as.dist’
HD2013SGIselectByStability: no visible global function definition for
 ‘lm’
HD2013SGIselectByStability : <anonymous>: no visible global function
 definition for ‘cor’
plotExampleInteractions: no visible binding for global variable ‘sd’
plotExampleInteractions: no visible global function definition for
 ‘par’
plotExampleInteractions: no visible global function definition for
 ‘barplot’
plotExampleInteractions: no visible global function definition for
 ‘abline’
plotExampleInteractions: no visible global function definition for
 ‘points’
plotExampleInteractions: no visible global function definition for
 ‘text’
plotExampleSingleGeneEffects: no visible global function definition for
 ‘mad’
plotExampleSingleGeneEffects: no visible global function definition for
 ‘par’
plotExampleSingleGeneEffects: no visible global function definition for
 ‘barplot’
plotExampleSingleGeneEffects: no visible global function definition for
 ‘abline’
plotExampleSingleGeneEffects: no visible global function definition for
 ‘points’
Undefined global functions or variables:
 abline as.dist barplot cor gpar grid.layout grid.raster grid.rect
 grid.text hclust lm mad median par points popViewport pushViewport sd
 text unit viewport
Consider adding
 importFrom("graphics", "abline", "barplot", "par", "points", "text")
 importFrom("stats", "as.dist", "cor", "hclust", "lm", "mad", "median",
 "sd")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
featuresPerWell 42.396 0.768 43.188
datamatrixfull 9.520 0.092 9.617
* 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: 4 NOTEs
See
 ‘/home/biocbuild/bbs-3.5-data-experiment/meat/HD2013SGI.Rcheck/00check.log’
for details.

* installing *source* package ‘HD2013SGI’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HD2013SGI)