ClassifyR 1.8.2
Dario Strbenac
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ClassifyR | | Last Changed Rev: 126579 / Revision: 128728 | | Last Changed Date: 2017-02-08 00:00:34 -0500 (Wed, 08 Feb 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf ClassifyR.buildbin-libdir ClassifyR.Rcheck && mkdir ClassifyR.buildbin-libdir ClassifyR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_1.8.2.tar.gz >ClassifyR.Rcheck\00install.out 2>&1 && cp ClassifyR.Rcheck\00install.out ClassifyR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ClassifyR.buildbin-libdir --install="check:ClassifyR-install.out" --force-multiarch --no-vignettes --timings ClassifyR_1.8.2.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ClassifyR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.8.2'
* 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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.doTest : <anonymous>: no visible global function definition for
'capture.output'
KolmogorovSmirnovSelection,ExpressionSet : <anonymous>: no visible
global function definition for 'ks.test'
PredictParams,ANY: no visible binding for global variable 'predict'
TrainParams,ANY: no visible binding for global variable 'dlda'
bartlettSelection,ExpressionSet : <anonymous>: no visible global
function definition for 'bartlett.test'
edgeRselection,ExpressionSet: no visible global function definition for
'model.matrix'
errorMap,list: no visible binding for global variable 'Class'
errorMap,list: no visible binding for global variable 'name'
errorMap,list: no visible binding for global variable 'type'
errorMap,list: no visible binding for global variable 'Error'
fisherDiscriminant,ExpressionSet: no visible binding for global
variable 'var'
getLocationsAndScales,ExpressionSet: no visible binding for global
variable 'median'
getLocationsAndScales,ExpressionSet: no visible binding for global
variable 'sd'
getLocationsAndScales,ExpressionSet: no visible binding for global
variable 'mad'
likelihoodRatioSelection,ExpressionSet : <anonymous>: no visible global
function definition for 'dnorm'
limmaSelection,ExpressionSet: no visible global function definition for
'model.matrix'
medianDifferenceSelection,ExpressionSet: no visible binding for global
variable 'median'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
<anonymous>: no visible global function definition for 'dnorm'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous>: no
visible binding for global variable 'classes'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
<anonymous> : <anonymous>: no visible binding for global variable
'largerClass'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
<anonymous> : <anonymous>: no visible binding for global variable
'classes'
naiveBayesKernel,ExpressionSet: no visible binding for global variable
'density'
naiveBayesKernel,ExpressionSet: no visible binding for global variable
'featureValues'
naiveBayesKernel,ExpressionSet : <anonymous>: no visible global
function definition for 'splinefun'
performancePlot,list: no visible global function definition for
'reformulate'
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
global variable 'expr'
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
global variable '..density..'
previousSelection,ExpressionSet: no visible global function definition
for 'na.omit'
rankingPlot,list: no visible global function definition for
'reformulate'
runTests,ExpressionSet: no visible global function definition for
'combn'
selectionPlot,list: no visible binding for global variable 'Freq'
selectionPlot,list: no visible global function definition for
'reformulate'
subtractFromLocation,ExpressionSet: no visible binding for global
variable 'median'
Undefined global functions or variables:
..density.. Class Error Freq bartlett.test capture.output classes
combn density dlda dnorm expr featureValues ks.test largerClass mad
median model.matrix na.omit name predict reformulate sd splinefun
type var
Consider adding
importFrom("stats", "bartlett.test", "density", "dnorm", "ks.test",
"mad", "median", "model.matrix", "na.omit", "predict",
"reformulate", "sd", "splinefun", "var")
importFrom("utils", "capture.output", "combn")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runTests 10.58 0.30 14.94
runTest 10.42 0.26 10.69
ClassifyResult-class 9.58 0.28 18.27
edgeRselection 8.50 0.26 8.94
distribution 6.52 0.14 11.27
likelihoodRatioSelection 5.75 0.07 5.83
DMDselection 5.39 0.08 5.46
KolmogorovSmirnovSelection 5.26 0.00 5.27
KullbackLeiblerSelection 5.03 0.00 5.03
previousSelection 0.11 0.02 5.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
edgeRselection 10.11 0.12 10.23
runTests 8.73 0.19 13.28
distribution 7.52 0.30 13.05
runTest 7.64 0.16 7.79
ClassifyResult-class 6.60 0.17 11.42
likelihoodRatioSelection 6.74 0.02 6.75
DMDselection 6.40 0.02 6.43
KolmogorovSmirnovSelection 5.99 0.00 5.98
KullbackLeiblerSelection 5.78 0.00 5.78
previousSelection 0.12 0.00 7.74
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.