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CHECK report for geNetClassifier on celaya2

This page was generated on 2019-04-09 13:07:19 -0400 (Tue, 09 Apr 2019).

Package 633/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.23.0
Sara Aibar
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/geNetClassifier
Branch: master
Last Commit: 800951a
Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: geNetClassifier
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geNetClassifier_1.23.0.tar.gz
StartedAt: 2019-04-09 02:12:46 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:14:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 101.9 seconds
RetCode: 0
Status:  OK 
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geNetClassifier_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/geNetClassifier.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.23.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.GeNetClassifierReturn plot.GenesNetwork plot.GenesRanking
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 4.422  0.751   5.306
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/geNetClassifier.Rcheck/00check.log’
for details.



Installation output

geNetClassifier.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL geNetClassifier
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘geNetClassifier’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (geNetClassifier)

Tests output

geNetClassifier.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("geNetClassifier")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

02:14:19 - Filtering data and calculating the genes ranking...
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset),  :
  The argument 'sampleLabels' had to be converted into a factor.
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset),  :
  The data labels vector is not named, it will be assumed the labels are in order: the first label applies to the first sample... 


RUNIT TEST PROTOCOL -- Tue Apr  9 02:14:19 2019 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geNetClassifier RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In geNetClassifier(matrix(sample(50000, 5 * 2), 5, 2), c(rep("one",  :
  The argument 'classification sampleLabels' had to be converted into a factor.
2: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  The argument 'classification sampleLabels' had to be converted into a factor.
3: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  The data labels vector is not named, it is assumed the labels are in order: the first label applies to the first sample... 
4: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  It is recommended to have the *same* number of samples in each class in order to obtain balanced external validation stats.
> 
> proc.time()
   user  system elapsed 
  1.304   0.234   1.488 

Example timings

geNetClassifier.Rcheck/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.8980.1521.055
GeneralizationError-class0.4950.0550.550
GenesNetwork-class2.8070.5243.373
GenesRanking-class0.8830.1140.996
calculateGenesRanking0.5820.0860.667
externalValidation.probMatrix0.9820.0921.071
externalValidation.stats1.0450.0971.141
gClasses-methods0.3240.0150.340
geNetClassifier0.1970.0420.238
geneSymbols0.1140.0040.117
genesDetails-methods0.4630.0460.509
getEdges-methods0.2730.0160.288
getNodes-methods0.3580.0160.375
getNumEdges-methods0.3340.0170.351
getNumNodes-methods0.3850.0220.407
getRanking-methods0.3770.0240.400
getSubNetwork-methods0.3490.0230.372
getTopRanking-methods0.3910.0220.413
leukemiasClassifier0.4110.0450.456
network2txt0.3700.0430.423
numGenes-methods0.3600.0150.375
numSignificantGenes-methods0.3430.0210.364
overview-methods0.3980.0350.432
plot.GeNetClassifierReturn4.4220.7515.306
plot.GenesRanking0.3540.0310.385
plotAssignments1.0460.0841.130
plotDiscriminantPower0.8730.1751.050
plotExpressionProfiles1.4230.1891.619
plotNetwork3.1250.4593.576
queryGeNetClassifier1.4730.1281.599
querySummary0.9080.0550.962