BioC 3.6: CHECK report for geNetClassifier on malbec1

Package: geNetClassifier

Version: 1.17.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.17.0.tar.gz

StartedAt: 2017-08-15 23:27:00 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:28:08 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 67.1 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.17.0’
* 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 ‘geNetClassifier’ 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 ... NOTE
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘igraph’ ‘infotheo’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateGenesRanking: no visible global function definition for
  ‘brewer.pal’
calculateGenesRanking: no visible global function definition for
  ‘rainbow’
calculateGenesRanking: no visible global function definition for
  ‘lines’
calculateGenesRanking: no visible global function definition for
  ‘title’
calculateGenesRanking: no visible global function definition for
  ‘abline’
calculateGenesRanking: no visible global function definition for ‘text’
calculateGenesRanking: no visible global function definition for
  ‘legend’
configurePlotOutput: no visible global function definition for ‘pdf’
configurePlotOutput: no visible global function definition for ‘par’
correlation.net: no visible global function definition for ‘cor’
geNetClassifier: no visible global function definition for
  ‘flush.console’
geNetClassifier : <anonymous>: no visible global function definition
  for ‘sd’
geNetClassifier : <anonymous>: no visible global function definition
  for ‘na.omit’
geNetClassifier: no visible global function definition for ‘sd’
geNetClassifier: no visible global function definition for ‘pdf’
geNetClassifier: no visible global function definition for ‘dev.off’
iqr.filter: no visible global function definition for ‘quantile’
plotAssignments: no visible global function definition for ‘rect’
plotAssignments: no visible global function definition for ‘abline’
plotAssignments: no visible global function definition for ‘axis’
plotAssignments: no visible global function definition for ‘text’
plotAssignments: no visible global function definition for ‘legend’
plotAssignments: no visible global function definition for ‘strwidth’
plotAssignments: no visible global function definition for ‘points’
plotAssignments: no visible global function definition for ‘dev.cur’
plotAssignments: no visible binding for global variable ‘coordinates’
plotDiscriminantPower: no visible global function definition for
  ‘colorRampPalette’
plotDiscriminantPower: no visible global function definition for
  ‘barplot’
plotDiscriminantPower: no visible global function definition for
  ‘abline’
plotDiscriminantPower: no visible global function definition for ‘text’
plotDiscriminantPower: no visible global function definition for ‘par’
plotDiscriminantPower: no visible global function definition for
  ‘dev.off’
plotDiscriminantPower: no visible global function definition for
  ‘flush.console’
plotErrorNumGenes: no visible global function definition for ‘pdf’
plotErrorNumGenes: no visible global function definition for
  ‘brewer.pal’
plotErrorNumGenes: no visible global function definition for ‘rainbow’
plotErrorNumGenes: no visible global function definition for ‘plot.new’
plotErrorNumGenes: no visible global function definition for
  ‘plot.window’
plotErrorNumGenes: no visible global function definition for ‘title’
plotErrorNumGenes: no visible global function definition for ‘axis’
plotErrorNumGenes: no visible global function definition for ‘lines’
plotErrorNumGenes: no visible global function definition for ‘points’
plotErrorNumGenes: no visible global function definition for ‘text’
plotErrorNumGenes: no visible global function definition for ‘barplot’
plotErrorNumGenes: no visible global function definition for ‘dev.off’
plotExpressionProfiles: no visible global function definition for ‘hcl’
plotExpressionProfiles: no visible global function definition for
  ‘setNames’
plotExpressionProfiles: no visible global function definition for
  ‘title’
plotExpressionProfiles: no visible global function definition for
  ‘text’
plotExpressionProfiles: no visible global function definition for
  ‘abline’
plotExpressionProfiles: no visible global function definition for
  ‘lines’
plotExpressionProfiles: no visible global function definition for
  ‘boxplot’
plotExpressionProfiles: no visible global function definition for ‘par’
plotExpressionProfiles: no visible global function definition for
  ‘dev.off’
plotExpressionProfiles: no visible global function definition for
  ‘flush.console’
plotExpressionProfiles: no visible global function definition for
  ‘dev.cur’
plotGeNetClassifierReturn: no visible global function definition for
  ‘pdf’
plotGeNetClassifierReturn: no visible global function definition for
  ‘dev.off’
plotGeNetClassifierReturn: no visible global function definition for
  ‘installed.packages’
plotGeNetClassifierReturn: no visible global function definition for
  ‘x11’
plotGeNetClassifierReturn: no visible global function definition for
  ‘flush.console’
plotNetwork: no visible global function definition for
  ‘installed.packages’
plotNetwork: no visible global function definition for ‘pdf’
plotNetwork: no visible global function definition for ‘par’
plotNetwork: no visible global function definition for
  ‘graph.data.frame’
plotNetwork: no visible global function definition for ‘vcount’
plotNetwork: no visible global function definition for
  ‘layout.fruchterman.reingold’
plotNetwork: no visible global function definition for
  ‘get.vertex.attribute’
plotNetwork: no visible global function definition for
  ‘colorRampPalette’
plotNetwork: no visible global function definition for
  ‘get.edge.attribute’
plotNetwork: no visible global function definition for ‘ecount’
plotNetwork: no visible global function definition for ‘tkplot’
plotNetwork: no visible global function definition for ‘plot.new’
plotNetwork: no visible global function definition for ‘title’
plotNetwork: no visible global function definition for ‘text’
plotNetwork: no visible global function definition for ‘points’
plotNetwork: no visible global function definition for ‘lines’
plotNetwork: no visible global function definition for ‘dev.off’
plotNetwork: no visible global function definition for ‘flush.console’
queryGeNetClassifier: no visible global function definition for
  ‘flush.console’
queryGeNetClassifier: no visible global function definition for
  ‘predict’
querySummary: no visible global function definition for ‘sd’
querySummary: no visible global function definition for ‘flush.console’
extractGenes,GenesRanking: no visible global function definition for
  ‘na.omit’
extractGenes,GenesRanking : <anonymous>: no visible global function
  definition for ‘na.omit’
network2txt,GenesNetwork: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline axis barplot boxplot brewer.pal colorRampPalette coordinates
  cor dev.cur dev.off ecount flush.console get.edge.attribute
  get.vertex.attribute graph.data.frame hcl installed.packages
  layout.fruchterman.reingold legend lines na.omit par pdf plot.new
  plot.window points predict quantile rainbow rect sd setNames strwidth
  text title tkplot vcount write.table x11
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.off",
             "hcl", "pdf", "rainbow", "x11")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "legend", "lines", "par", "plot.new", "plot.window",
             "points", "rect", "strwidth", "text", "title")
  importFrom("stats", "cor", "na.omit", "predict", "quantile", "sd",
             "setNames")
  importFrom("utils", "flush.console", "installed.packages",
             "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.6-bioc/meat/geNetClassifier.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GeNetClassifierReturn-class	1.080	0.048	1.312
GeneralizationError-class	0.456	0.068	0.527
GenesNetwork-class	1.768	0.116	1.959
GenesRanking-class	0.656	0.052	0.707
calculateGenesRanking	1.440	0.072	1.515
externalValidation.probMatrix	0.760	0.024	0.786
externalValidation.stats	1.028	0.020	1.051
gClasses-methods	0.404	0.024	0.427
geNetClassifier	0.144	0.008	0.150
geneSymbols	0.072	0.000	0.070
genesDetails-methods	0.356	0.016	0.374
getEdges-methods	0.236	0.024	0.262
getNodes-methods	0.256	0.012	0.265
getNumEdges-methods	0.240	0.020	0.262
getNumNodes-methods	0.288	0.024	0.312
getRanking-methods	0.272	0.020	0.291
getSubNetwork-methods	0.284	0.020	0.304
getTopRanking-methods	0.260	0.000	0.259
leukemiasClassifier	0.320	0.012	0.333
network2txt	0.320	0.020	0.341
numGenes-methods	0.244	0.024	0.268
numSignificantGenes-methods	0.272	0.020	0.292
overview-methods	0.396	0.024	0.419
plot.GeNetClassifierReturn	4.036	0.124	4.210
plot.GenesRanking	0.272	0.016	0.291
plotAssignments	0.716	0.048	0.768
plotDiscriminantPower	0.616	0.052	0.668
plotExpressionProfiles	1.416	0.048	1.458
plotNetwork	2.056	0.068	2.124
queryGeNetClassifier	0.968	0.044	1.019
querySummary	0.768	0.036	0.807