BioC 3.5: CHECK report for RNAinteract on veracruz2

Package: RNAinteract

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAinteract_1.24.0.tar.gz

StartedAt: 2017-10-18 08:25:58 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:29:17 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 199.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAinteract.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAinteract_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RNAinteract.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAinteract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAinteract’ version ‘1.24.0’
* 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 ‘RNAinteract’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ICS’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘abind’ ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindscreens: no visible global function definition for ‘is’
bindscreens: no visible global function definition for ‘abind’
computePValues : <anonymous>: no visible global function definition for
  ‘p.adjust’
computePValues: no visible global function definition for ‘is’
computePValues: no visible binding for global variable ‘sd’
computePValues: no visible global function definition for ‘median’
computePValues: no visible global function definition for ‘pt’
createCellHTSFromFiles: no visible global function definition for
  ‘read.table’
createCellHTSFromFiles: no visible binding for global variable ‘df’
createCellHTSFromFiles: no visible binding for global variable
  ‘assayDataNew’
createCellHTSFromFiles: no visible global function definition for ‘new’
createCellHTSFromFiles: no visible global function definition for
  ‘getClassDef’
createRNAinteract: no visible global function definition for ‘new’
createRNAinteractFromFiles: no visible global function definition for
  ‘read.table’
embedPCA: no visible global function definition for ‘prcomp’
estimateMainEffect: no visible global function definition for ‘is’
estimateMainEffect: no visible binding for global variable ‘median’
estimateMainEffect: no visible binding for global variable ‘mad’
estimateMainEffect: no visible global function definition for ‘median’
getChannelNames: no visible global function definition for ‘is’
getData: no visible global function definition for ‘is’
getIndDesignData: no visible global function definition for ‘is’
getInvTransformation: no visible global function definition for ‘is’
getMain: no visible global function definition for ‘is’
getReplicateData: no visible global function definition for ‘is’
getScale: no visible global function definition for ‘is’
getScreenNames: no visible global function definition for ‘is’
getTransformation: no visible global function definition for ‘is’
grid.sgiColorkey: no visible global function definition for
  ‘colorRampPalette’
grid.sgiColorkey: no visible global function definition for ‘col2rgb’
grid.sgiColorkey: no visible global function definition for ‘mad’
grid.sgiColorkey: no visible global function definition for ‘quantile’
grid.sgiDendrogram: no visible global function definition for
  ‘as.dendrogram’
grid.sgiDendrogram: no visible global function definition for
  ‘order.dendrogram’
grid.sgiHeatmap.2: no visible global function definition for ‘hclust’
grid.sgiHeatmap.2: no visible global function definition for ‘dist’
grid.sgiHeatmap.2: no visible global function definition for
  ‘as.dendrogram’
grid.sgiHeatmap.2: no visible global function definition for
  ‘order.dendrogram’
grid.sgiHeatmap.2: no visible global function definition for
  ‘colorRampPalette’
grid.sgiHeatmap.2: no visible global function definition for ‘mad’
grid.sgiHeatmap.2: no visible global function definition for ‘quantile’
grid.sgiHeatmap.2: no visible binding for global variable ‘C’
makeDoublePerturbationPoints: no visible global function definition for
  ‘rainbow’
makeDoublePerturbationPoints: no visible global function definition for
  ‘colorRampPalette’
normalizeMainEffectQuery: no visible global function definition for
  ‘is’
normalizeMainEffectQuery: no visible global function definition for
  ‘lm’
normalizeMainEffectQuery: no visible global function definition for
  ‘predict’
normalizeMainEffectTemplate: no visible global function definition for
  ‘is’
normalizeMainEffectTemplate: no visible global function definition for
  ‘medpolish’
normalizePlateEffect: no visible global function definition for ‘is’
normalizePlateEffect: no visible global function definition for ‘sd’
normalizePlateEffect: no visible global function definition for
  ‘medpolish’
normalizePlateEffect: no visible global function definition for
  ‘locfit’
normalizePlateEffect: no visible binding for global variable
  ‘locfit.robust’
normalizePlateEffect: no visible global function definition for
  ‘predict’
plotDoublePerturbation: no visible global function definition for ‘is’
plotDoublePerturbation: no visible global function definition for ‘mad’
plotHeatmap: no visible global function definition for ‘is’
plotIndDesignScatter: no visible global function definition for ‘is’
plotIndDesignScatter: no visible global function definition for
  ‘smoothScatter’
plotMainEffects: no visible global function definition for ‘rainbow’
plotMainEffects: no visible global function definition for ‘is’
plotReplicateScatter: no visible global function definition for ‘is’
plotReplicateScatter: no visible global function definition for
  ‘smoothScatter’
plotScatterErrorbars: no visible global function definition for
  ‘rainbow’
plotScatterErrorbars: no visible global function definition for ‘plot’
plotScatterErrorbars: no visible global function definition for
  ‘points’
plotScatterErrorbars: no visible global function definition for
  ‘legend’
plotScreenData: no visible global function definition for ‘is’
plotScreenData: no visible global function definition for ‘median’
reportAnnotation: no visible global function definition for ‘is’
reportAnnotation: no visible global function definition for
  ‘write.table’
reportDoublePerturbation: no visible global function definition for
  ‘is’
reportDoublePerturbation: no visible global function definition for
  ‘png’
reportDoublePerturbation: no visible global function definition for
  ‘dev.off’
reportDoublePerturbation: no visible global function definition for
  ‘pdf’
reportGeneLists: no visible global function definition for ‘is’
reportGeneLists: no visible global function definition for
  ‘write.table’
reportHeatmap: no visible global function definition for ‘is’
reportHeatmap: no visible global function definition for ‘png’
reportHeatmap: no visible global function definition for ‘dev.off’
reportHeatmap: no visible global function definition for ‘pdf’
reportMainEffects: no visible global function definition for ‘is’
reportMainEffects: no visible global function definition for ‘png’
reportMainEffects: no visible global function definition for ‘dev.off’
reportMainEffects: no visible global function definition for ‘pdf’
reportMainEffects: no visible global function definition for ‘plot’
reportMainEffects: no visible global function definition for ‘points’
reportNetworks: no visible global function definition for ‘is’
reportNetworks: no visible global function definition for ‘fisher.test’
reportNetworks: no visible global function definition for ‘png’
reportNetworks: no visible global function definition for ‘par’
reportNetworks: no visible global function definition for ‘dev.off’
reportNetworks: no visible global function definition for ‘pdf’
reportNetworks: no visible global function definition for ‘write.table’
reportScreenData: no visible global function definition for ‘is’
reportScreenData: no visible global function definition for ‘png’
reportScreenData: no visible global function definition for ‘dev.off’
reportScreenData: no visible global function definition for ‘pdf’
reportStatistics: no visible global function definition for ‘is’
reportStatistics: no visible global function definition for ‘png’
reportStatistics: no visible global function definition for ‘plot’
reportStatistics: no visible global function definition for ‘points’
reportStatistics: no visible global function definition for ‘legend’
reportStatistics: no visible global function definition for ‘dev.off’
reportStatistics: no visible global function definition for ‘pdf’
reportStatistics: no visible global function definition for
  ‘write.table’
reportStatistics: no visible global function definition for ‘cor’
reportStatistics: no visible global function definition for
  ‘smoothScatter’
sgisubset: no visible global function definition for ‘is’
sgisubsetQueryDesign: no visible global function definition for ‘is’
shiftboxes: no visible global function definition for ‘median’
summarizeScreens: no visible global function definition for ‘is’
Undefined global functions or variables:
  C abind as.dendrogram assayDataNew col2rgb colorRampPalette cor
  dev.off df dist fisher.test getClassDef hclust is legend lm locfit
  locfit.robust mad median medpolish new order.dendrogram p.adjust par
  pdf plot png points prcomp predict pt quantile rainbow read.table sd
  smoothScatter write.table
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
             "pdf", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points",
             "smoothScatter")
  importFrom("methods", "getClassDef", "is", "new")
  importFrom("stats", "C", "as.dendrogram", "cor", "df", "dist",
             "fisher.test", "hclust", "lm", "mad", "median", "medpolish",
             "order.dendrogram", "p.adjust", "prcomp", "predict", "pt",
             "quantile", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RNAinteract.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAinteract’ ...
** 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 (RNAinteract)

name	user	system	elapsed
RNAinteract-class	0.003	0.001	0.004
bindsamples	0.428	0.031	0.471
computePI	0.258	0.003	0.268
computePValues	0.242	0.004	0.253
embedPCA	0.013	0.001	0.016
estimateMainEffect	1.069	0.010	1.114
getData	0.333	0.005	0.351
getMain	0.153	0.005	0.160
getReplicateData	0.031	0.002	0.034
getSampleNames	0.005	0.001	0.007
getScale	0.006	0.001	0.007
grid.sgiHeatmap	0.075	0.003	0.081
normalizeMainEffectQuery	0.058	0.001	0.060
normalizeMainEffectTemplate	0.050	0.002	0.054
normalizePlateEffect	1.713	0.030	1.812
plotDoublePerturbation	0.200	0.002	0.208
plotHeatmap	0.180	0.002	0.193
reportAnnotation	0.293	0.004	0.299
sgi	0.006	0.001	0.007
sgisubset	0.084	0.002	0.087
startReport	0.054	0.002	0.056
summarizeSamples	0.278	0.002	0.288