BioC 3.5: CHECK report for geNetClassifier on tokay2

Package: geNetClassifier

Version: 1.16.0

Command: rm -rf geNetClassifier.buildbin-libdir geNetClassifier.Rcheck && mkdir geNetClassifier.buildbin-libdir geNetClassifier.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geNetClassifier.buildbin-libdir geNetClassifier_1.16.0.tar.gz >geNetClassifier.Rcheck\00install.out 2>&1 && cp geNetClassifier.Rcheck\00install.out geNetClassifier-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=geNetClassifier.buildbin-libdir --install="check:geNetClassifier-install.out" --force-multiarch --no-vignettes --timings geNetClassifier_1.16.0.tar.gz

StartedAt: 2017-08-15 23:59:48 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-16 00:02:02 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 134.4 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf geNetClassifier.buildbin-libdir geNetClassifier.Rcheck && mkdir geNetClassifier.buildbin-libdir geNetClassifier.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geNetClassifier.buildbin-libdir geNetClassifier_1.16.0.tar.gz >geNetClassifier.Rcheck\00install.out 2>&1 && cp geNetClassifier.Rcheck\00install.out geNetClassifier-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=geNetClassifier.buildbin-libdir --install="check:geNetClassifier-install.out" --force-multiarch --no-vignettes --timings geNetClassifier_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/geNetClassifier.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' version '1.16.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/geNetClassifier.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'geNetClassifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geNetClassifier' as geNetClassifier_1.16.0.zip
* DONE (geNetClassifier)

name	user	system	elapsed
GeNetClassifierReturn-class	1.52	0.04	3.22
GeneralizationError-class	0.76	0.02	0.78
GenesNetwork-class	1.69	0.23	2.01
GenesRanking-class	0.78	0.02	0.80
calculateGenesRanking	1.19	0.03	1.24
externalValidation.probMatrix	0.66	0.02	0.67
externalValidation.stats	0.65	0.06	0.72
gClasses-methods	0.28	0.00	0.28
geNetClassifier	0.19	0.02	0.20
geneSymbols	0.08	0.00	0.08
genesDetails-methods	0.37	0.01	0.39
getEdges-methods	0.28	0.02	0.30
getNodes-methods	0.27	0.01	0.28
getNumEdges-methods	0.28	0.00	0.28
getNumNodes-methods	0.28	0.00	0.28
getRanking-methods	0.32	0.00	0.31
getSubNetwork-methods	0.29	0.02	0.32
getTopRanking-methods	0.31	0.00	0.31
leukemiasClassifier	0.36	0.03	0.39
network2txt	0.54	0.01	0.55
numGenes-methods	0.48	0.02	0.50
numSignificantGenes-methods	0.36	0.02	0.37
overview-methods	0.31	0.01	0.33
plot.GeNetClassifierReturn	3.24	0.10	3.34
plot.GenesRanking	0.51	0.03	0.55
plotAssignments	0.74	0.04	0.78
plotDiscriminantPower	0.71	0.03	0.75
plotExpressionProfiles	1.54	0.05	1.58
plotNetwork	2.50	0.03	2.53
queryGeNetClassifier	0.87	0.02	0.89
querySummary	0.64	0.06	0.70

name	user	system	elapsed
GeNetClassifierReturn-class	1.03	0.02	1.04
GeneralizationError-class	0.49	0.03	0.52
GenesNetwork-class	1.66	0.31	2.05
GenesRanking-class	0.75	0.00	0.75
calculateGenesRanking	1.25	0.04	1.30
externalValidation.probMatrix	0.69	0.00	0.68
externalValidation.stats	1.01	0.01	1.04
gClasses-methods	0.28	0.02	0.29
geNetClassifier	0.16	0.00	0.16
geneSymbols	0.08	0.00	0.08
genesDetails-methods	0.42	0.00	0.42
getEdges-methods	0.39	0.01	0.41
getNodes-methods	0.33	0.02	0.34
getNumEdges-methods	0.28	0.01	0.30
getNumNodes-methods	0.28	0.00	0.28
getRanking-methods	0.43	0.02	0.46
getSubNetwork-methods	0.29	0.01	0.29
getTopRanking-methods	0.28	0.00	0.29
leukemiasClassifier	0.31	0.02	0.32
network2txt	0.45	0.00	0.46
numGenes-methods	0.27	0.00	0.26
numSignificantGenes-methods	0.26	0.00	0.27
overview-methods	0.31	0.00	0.32
plot.GeNetClassifierReturn	4.31	0.08	4.39
plot.GenesRanking	0.38	0.00	0.38
plotAssignments	0.79	0.00	0.79
plotDiscriminantPower	0.77	0.05	0.82
plotExpressionProfiles	1.67	0.03	1.70
plotNetwork	2.89	0.03	2.92
queryGeNetClassifier	0.83	0.06	0.89
querySummary	0.67	0.00	0.67