BioC 3.4: CHECK report for geNetClassifier on malbec1

Package: geNetClassifier

Version: 1.14.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.14.0.tar.gz

StartedAt: 2017-04-14 22:45:19 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:46:20 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 60.3 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.0’
* 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-3.4-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	0.756	0.028	0.981
GeneralizationError-class	0.448	0.000	0.446
GenesNetwork-class	1.016	0.040	1.062
GenesRanking-class	0.596	0.032	0.627
calculateGenesRanking	0.508	0.008	0.518
externalValidation.probMatrix	0.772	0.008	0.779
externalValidation.stats	0.676	0.004	0.681
gClasses-methods	0.236	0.004	0.239
geNetClassifier	0.212	0.000	0.209
geneSymbols	0.068	0.000	0.065
genesDetails-methods	0.344	0.008	0.354
getEdges-methods	0.264	0.004	0.270
getNodes-methods	0.240	0.004	0.244
getNumEdges-methods	0.248	0.000	0.251
getNumNodes-methods	0.248	0.000	0.247
getRanking-methods	0.288	0.000	0.291
getSubNetwork-methods	0.268	0.000	0.269
getTopRanking-methods	0.260	0.000	0.258
leukemiasClassifier	0.296	0.004	0.301
network2txt	0.340	0.012	0.350
numGenes-methods	0.252	0.000	0.249
numSignificantGenes-methods	0.244	0.004	0.249
overview-methods	0.296	0.004	0.298
plot.GeNetClassifierReturn	4.680	0.128	4.845
plot.GenesRanking	0.272	0.000	0.275
plotAssignments	0.684	0.008	0.699
plotDiscriminantPower	0.652	0.004	0.658
plotExpressionProfiles	1.172	0.012	1.192
plotNetwork	2.600	0.052	2.644
queryGeNetClassifier	1.008	0.004	1.011
querySummary	0.700	0.008	0.706