geNetClassifier 1.16.0
Sara Aibar
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/geNetClassifier | | Branch: RELEASE_3_5 | | Last Commit: a99767b | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.16.0’
* 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 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 ... ERROR
Running examples in ‘geNetClassifier-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GenesNetwork-class
> ### Title: Class "GenesNetwork"
> ### Aliases: GenesNetwork GenesNetwork-class initialize,GenesNetwork-method
> ### show,GenesNetwork-method
> ### Keywords: classes
>
> ### ** Examples
>
> ######
> # Load data and train a classifier
> ######
>
> # Load an expressionSet:
> library(leukemiasEset)
> data(leukemiasEset)
>
> # Select the train samples:
> trainSamples<- c(1:10, 13:22, 25:34, 37:46, 49:58)
> # summary(leukemiasEset$LeukemiaType[trainSamples])
>
> # Train a classifier or load a trained one:
> # leukemiasClassifier <- geNetClassifier(leukemiasEset[,trainSamples],
> # sampleLabels="LeukemiaType", plotsName="leukemiasClassifier")
> data(leukemiasClassifier) # Sample trained classifier
>
> ######
> # Explore the returned object
> ######
> # Global view of the object and its structure:
> names(leukemiasClassifier)
[1] "call" "classifier" "classificationGenes"
[4] "generalizationError" "genesRanking" "genesRankingType"
[7] "genesNetwork" "genesNetworkType"
>
> # List of Networks by classes:
> leukemiasClassifier@genesNetwork
$ALL
Attribute summary of the GenesNetwork:
Number of nodes (genes): [1] 1027
Number of edges (relationships): [1] 1942
$AML
Attribute summary of the GenesNetwork:
Number of nodes (genes): [1] 400
Number of edges (relationships): [1] 296
$CLL
Attribute summary of the GenesNetwork:
Number of nodes (genes): [1] 1916
Number of edges (relationships): [1] 18506
$CML
Attribute summary of the GenesNetwork:
Number of nodes (genes): [1] 949
Number of edges (relationships): [1] 6540
$NoL
Attribute summary of the GenesNetwork:
Number of nodes (genes): [1] 400
Number of edges (relationships): [1] 1993
> # Access to the nodes or edges of each network:
> getEdges(leukemiasClassifier@genesNetwork$AML)[1:5,]
gene1 class1 gene2 class2 relation
[1,] "ENSG00000078399" "AML" "ENSG00000143995" "AML" "Correlation - pearson"
[2,] "ENSG00000154188" "AML" "ENSG00000198795" "AML" "Correlation - pearson"
[3,] "ENSG00000078399" "AML" "ENSG00000106004" "AML" "Correlation - pearson"
[4,] "ENSG00000154188" "AML" "ENSG00000155792" "AML" "Correlation - pearson"
[5,] "ENSG00000119919" "AML" "ENSG00000108511" "AML" "Correlation - pearson"
value
[1,] "0.922460476283629"
[2,] "0.804443836092871"
[3,] "0.836149615702043"
[4,] "0.815177435058601"
[5,] "0.940367679337551"
> getNodes(leukemiasClassifier@genesNetwork$AML)[1:50]
[1] "ENSG00000078399" "ENSG00000143995" "ENSG00000185275" "ENSG00000154188"
[5] "ENSG00000133101" "ENSG00000198795" "ENSG00000106004" "ENSG00000155792"
[9] "ENSG00000119919" "ENSG00000106236" "ENSG00000148154" "ENSG00000108511"
[13] "ENSG00000012779" "ENSG00000177508" "ENSG00000092529" "ENSG00000111057"
[17] "ENSG00000153807" "ENSG00000165072" "ENSG00000197576" "ENSG00000128805"
[21] "ENSG00000122592" "ENSG00000105991" "ENSG00000185559" "ENSG00000087245"
[25] "ENSG00000151491" "ENSG00000003436" "ENSG00000152580" "ENSG00000167236"
[29] "ENSG00000233101" "ENSG00000134138" "ENSG00000121690" "ENSG00000163106"
[33] "ENSG00000145777" "ENSG00000164120" "ENSG00000147465" "ENSG00000180044"
[37] "ENSG00000052126" "ENSG00000115183" "ENSG00000113396" "ENSG00000171502"
[41] "ENSG00000179241" "ENSG00000003096" "ENSG00000120093" "ENSG00000180767"
[45] "ENSG00000183691" "ENSG00000020181" "ENSG00000087495" "ENSG00000179542"
[49] "ENSG00000157303" "ENSG00000147650"
>
>
> ######
> # Plotting
> ######
> # Example: Plotting the sub-network of a class classificationGenes
> # Get the sub-network containing only the classification genes:
> subNet <- getSubNetwork(leukemiasClassifier@genesNetwork,
+ leukemiasClassifier@classificationGenes)
> # Get the classification genes' info/details:
> clGenesInfo <- genesDetails(leukemiasClassifier@classificationGenes)
>
> # Plot the network of the class "ALL"
> plotNetwork(subNet$ALL, genesInfo=clGenesInfo,
+ plotOnlyConnectedNodesNetwork=FALSE)
Attaching package: ‘igraph’
The following objects are masked from ‘package:BiocGenerics’:
normalize, union
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
[tcl] invalid command name "font".
Calls: plotNetwork ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/geNetClassifier.Rcheck/00check.log’
for details.