##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ClassifyR_2.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ClassifyR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ClassifyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClassifyR' version '2.6.1'
* 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 'ClassifyR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmps1clUt/R.INSTALL27d824447e8f/ClassifyR/man/differentMeansSelection.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmps1clUt/R.INSTALL27d824447e8f/ClassifyR/man/distribution.Rd:32: file link 'stat_density' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmps1clUt/R.INSTALL27d824447e8f/ClassifyR/man/edgeRselection.Rd:45: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ClassifyR.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.posterior_probs : <anonymous>: no visible global function definition
for 'dmvnorm'
easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no
visible binding for global variable 'measurements'
kTSPclassifier,DataFrame : <anonymous>: no visible global function
definition for 'Pairs'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'measurement'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable '..density..'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'legends grouping'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'key'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'value'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable 'ID'
rankingPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'first'
rankingPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'second'
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'first'
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'second'
runTest,DataFrame: no visible binding for global variable 'setsNodes'
runTestEasyHard,MultiAssayExperiment: no visible binding for global
variable 'setsNodes'
runTests,DataFrame: no visible binding for global variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
variable '.iteration'
samplesMetricMap,list: no visible binding for global variable 'Class'
samplesMetricMap,list: no visible binding for global variable 'Group'
samplesMetricMap,list: no visible binding for global variable
'measurements'
samplesMetricMap,list: no visible binding for global variable 'name'
samplesMetricMap,list: no visible binding for global variable 'type'
samplesMetricMap,list: no visible binding for global variable 'Metric'
samplesMetricMap,matrix: no visible binding for global variable 'Class'
samplesMetricMap,matrix: no visible binding for global variable 'Group'
samplesMetricMap,matrix: no visible binding for global variable
'measurements'
samplesMetricMap,matrix: no visible binding for global variable 'name'
samplesMetricMap,matrix: no visible binding for global variable 'type'
samplesMetricMap,matrix: no visible binding for global variable
'Metric'
selectionPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'first'
selectionPlot,list : <anonymous> : <anonymous>: no visible global
function definition for 'second'
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for 'first'
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for 'second'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
..density.. .iteration Class Freq Group ID Metric Pairs dmvnorm first
key legends grouping measurement measurements name second setsNodes
type value
Consider adding
importFrom("base", "grouping")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'ClassifyR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runTests
> ### Title: Reproducibly Run Various Kinds of Cross-Validation
> ### Aliases: runTests runTestsEasyHard runTests,matrix-method
> ### runTests,DataFrame-method runTests,MultiAssayExperiment-method
> ### runTestsEasyHard,MultiAssayExperiment-method
>
> ### ** Examples
>
> #if(require(sparsediscrim))
> #{
> data(asthma)
>
> resubstituteParams <- ResubstituteParams(nFeatures = seq(5, 25, 5),
+ performanceType = "balanced error",
+ better = "lower")
> runTests(measurements, classes, datasetName = "Asthma",
+ classificationName = "Different Means", permutations = 5,
+ params = list(SelectParams(differentMeansSelection, "t Statistic",
+ resubstituteParams = resubstituteParams),
+ TrainParams(DLDAtrainInterface),
+ PredictParams(DLDApredictInterface)
+ )
+ )
An object of class 'ClassifyResult'.
Data Set Name: Asthma.
Classification Name: Different Means.
Feature Selection Name: t Statistic.
Features: List of length 5 of lists of length 5 of feature identifiers.
Validation: 5 Permutations, 5 Folds.
Predictions: List of data frames of length 5.
Performance Measures: None calculated yet.
> #}
>
> genesMatrix <- matrix(c(rnorm(90, 9, 1),
+ 9.5, 9.4, 5.2, 5.3, 5.4, 9.4, 9.6, 9.9, 9.1, 9.8),
+ ncol = 10, byrow = TRUE)
>
> colnames(genesMatrix) <- paste("Sample", 1:10)
> rownames(genesMatrix) <- paste("Gene", 1:10)
> genders <- factor(c("Male", "Male", "Female", "Female", "Female",
+ "Female", "Female", "Female", "Female", "Female"))
>
> # Scenario: Male gender can predict the hard-to-classify Sample 1 and Sample 2.
> clinical <- DataFrame(age = c(31, 34, 32, 39, 33, 38, 34, 37, 35, 36),
+ gender = genders,
+ class = factor(rep(c("Poor", "Good"), each = 5)),
+ row.names = colnames(genesMatrix))
> dataset <- MultiAssayExperiment(ExperimentList(RNA = genesMatrix), clinical)
> selParams <- SelectParams(featureSelection = differentMeansSelection, selectionName = "Difference in Means",
+ resubstituteParams = ResubstituteParams(1:10, "balanced error", "lower"))
> easyHardCV <- runTestsEasyHard(dataset, datasetName = "Test Data", classificationName = "Easy-Hard",
+ easyClassifierParams = list(minCardinality = 2, minPurity = 0.9),
+ hardClassifierParams = list(selParams, TrainParams(), PredictParams()),
+ validation = "leaveOut", leave = 1)
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: object 'selParams' not found
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'ClassifyR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runTests
> ### Title: Reproducibly Run Various Kinds of Cross-Validation
> ### Aliases: runTests runTestsEasyHard runTests,matrix-method
> ### runTests,DataFrame-method runTests,MultiAssayExperiment-method
> ### runTestsEasyHard,MultiAssayExperiment-method
>
> ### ** Examples
>
> #if(require(sparsediscrim))
> #{
> data(asthma)
>
> resubstituteParams <- ResubstituteParams(nFeatures = seq(5, 25, 5),
+ performanceType = "balanced error",
+ better = "lower")
> runTests(measurements, classes, datasetName = "Asthma",
+ classificationName = "Different Means", permutations = 5,
+ params = list(SelectParams(differentMeansSelection, "t Statistic",
+ resubstituteParams = resubstituteParams),
+ TrainParams(DLDAtrainInterface),
+ PredictParams(DLDApredictInterface)
+ )
+ )
An object of class 'ClassifyResult'.
Data Set Name: Asthma.
Classification Name: Different Means.
Feature Selection Name: t Statistic.
Features: List of length 5 of lists of length 5 of feature identifiers.
Validation: 5 Permutations, 5 Folds.
Predictions: List of data frames of length 5.
Performance Measures: None calculated yet.
> #}
>
> genesMatrix <- matrix(c(rnorm(90, 9, 1),
+ 9.5, 9.4, 5.2, 5.3, 5.4, 9.4, 9.6, 9.9, 9.1, 9.8),
+ ncol = 10, byrow = TRUE)
>
> colnames(genesMatrix) <- paste("Sample", 1:10)
> rownames(genesMatrix) <- paste("Gene", 1:10)
> genders <- factor(c("Male", "Male", "Female", "Female", "Female",
+ "Female", "Female", "Female", "Female", "Female"))
>
> # Scenario: Male gender can predict the hard-to-classify Sample 1 and Sample 2.
> clinical <- DataFrame(age = c(31, 34, 32, 39, 33, 38, 34, 37, 35, 36),
+ gender = genders,
+ class = factor(rep(c("Poor", "Good"), each = 5)),
+ row.names = colnames(genesMatrix))
> dataset <- MultiAssayExperiment(ExperimentList(RNA = genesMatrix), clinical)
> selParams <- SelectParams(featureSelection = differentMeansSelection, selectionName = "Difference in Means",
+ resubstituteParams = ResubstituteParams(1:10, "balanced error", "lower"))
> easyHardCV <- runTestsEasyHard(dataset, datasetName = "Test Data", classificationName = "Easy-Hard",
+ easyClassifierParams = list(minCardinality = 2, minPurity = 0.9),
+ hardClassifierParams = list(selParams, TrainParams(), PredictParams()),
+ validation = "leaveOut", leave = 1)
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: object 'selParams' not found
Execution halted
* 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 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.
