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CHECK report for geNetClassifier on malbec1

This page was generated on 2018-04-12 13:11:06 -0400 (Thu, 12 Apr 2018).

Package 550/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.18.0
Sara Aibar
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/geNetClassifier
Branch: RELEASE_3_6
Last Commit: 8749315
Last Changed Date: 2017-10-30 12:40:02 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geNetClassifier
Version: 1.18.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.18.0.tar.gz
StartedAt: 2018-04-11 23:46:16 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:47:22 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 66.6 seconds
RetCode: 0
Status:  OK 
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.18.0’
* 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.



Installation output

geNetClassifier.Rcheck/00install.out

* 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)

Tests output

geNetClassifier.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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")'.

23:47:18 - 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 -- Wed Apr 11 23:47:18 2018 
*********************************************** 
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 
  1.984   0.036   2.012 

Example timings

geNetClassifier.Rcheck/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.9640.0241.090
GeneralizationError-class0.5200.0160.537
GenesNetwork-class1.8640.1122.055
GenesRanking-class0.6760.0320.710
calculateGenesRanking1.5320.0441.593
externalValidation.probMatrix0.7800.0240.814
externalValidation.stats0.8160.0240.841
gClasses-methods0.2320.0000.235
geNetClassifier0.1560.0000.161
geneSymbols0.0760.0000.075
genesDetails-methods0.3600.0120.374
getEdges-methods0.2560.0000.257
getNodes-methods0.2520.0080.258
getNumEdges-methods0.2400.0120.252
getNumNodes-methods0.2480.0040.254
getRanking-methods0.2800.0000.282
getSubNetwork-methods0.2960.0000.293
getTopRanking-methods0.2480.0040.253
leukemiasClassifier0.3200.0040.324
network2txt0.3280.0080.336
numGenes-methods0.2520.0040.257
numSignificantGenes-methods0.2640.0040.270
overview-methods0.3880.0120.398
plot.GeNetClassifierReturn4.2600.1564.445
plot.GenesRanking0.3640.0040.370
plotAssignments0.8800.0160.898
plotDiscriminantPower0.7720.0000.769
plotExpressionProfiles1.4160.0481.455
plotNetwork2.2320.0722.322
queryGeNetClassifier1.2040.0321.242
querySummary0.7920.0120.806