Dario Strbenac
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ClassifyR |
| Branch: master |
| Last Commit: 8091e0b |
| Last Changed Date: 2019-01-22 19:41:20 -0400 (Tue, 22 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:11:20 -0400 (Tue, 09 Apr 2019).
| Package 275/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ClassifyR 2.3.6 Dario Strbenac
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: ClassifyR |
| Version: 2.3.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.3.6.tar.gz |
| StartedAt: 2019-04-09 00:43:00 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:50:46 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 466.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.3.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.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 ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘2.3.6’
* 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 ‘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
* 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’
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’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
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.. 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ClassifyResult-class 159.966 13.064 46.620
elasticNetGLMinterface 57.490 9.535 25.173
distribution 27.399 12.377 14.316
runTests 23.815 9.557 12.790
likelihoodRatioSelection 11.188 0.449 11.657
DMDselection 9.746 0.545 10.291
previousTrained 5.795 3.987 4.973
previousSelection 5.767 3.965 4.936
samplesMetricMap 7.762 0.570 8.363
edgeRselection 7.022 0.692 7.719
selectionPlot 5.352 0.822 6.072
rankingPlot 4.610 1.011 5.383
plotFeatureClasses 5.080 0.049 5.130
elasticNetFeatures 0.269 0.151 24.270
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.
ClassifyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ClassifyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ClassifyR’ ... ** 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 (ClassifyR)
ClassifyR.Rcheck/ClassifyR-Ex.timings
| name | user | system | elapsed | |
| ClassifyResult-class | 159.966 | 13.064 | 46.620 | |
| DLDAinterface | 0.100 | 0.003 | 0.103 | |
| DMDselection | 9.746 | 0.545 | 10.291 | |
| FeatureSetCollection-class | 0.009 | 0.002 | 0.011 | |
| FeatureSetCollectionOrNULL-class | 0.004 | 0.001 | 0.006 | |
| KolmogorovSmirnovSelection | 2.425 | 0.054 | 2.478 | |
| KullbackLeiblerSelection | 1.660 | 0.031 | 1.691 | |
| NSCpredictInterface | 0.229 | 0.015 | 0.250 | |
| NSCselectionInterface | 0.160 | 0.005 | 0.165 | |
| NSCtrainInterface | 0.138 | 0.005 | 0.143 | |
| PredictParams-class | 0.003 | 0.000 | 0.004 | |
| ROCplot | 1.393 | 0.059 | 1.454 | |
| ResubstituteParams-class | 0.003 | 0.001 | 0.004 | |
| SVMinterface | 0.092 | 0.004 | 0.097 | |
| SelectParams-class | 0.020 | 0.004 | 0.025 | |
| SelectResult-class | 0.002 | 0.001 | 0.003 | |
| TrainParams-class | 0.001 | 0.001 | 0.002 | |
| TransformParams-class | 0.003 | 0.000 | 0.003 | |
| bartlettSelection | 2.593 | 0.029 | 2.622 | |
| calcPerformance | 0.006 | 0.001 | 0.007 | |
| characterOrDataFrame-class | 0.013 | 0.001 | 0.013 | |
| classifyInterface | 0.910 | 0.254 | 1.167 | |
| differentMeansSelection | 2.059 | 0.052 | 2.109 | |
| distribution | 27.399 | 12.377 | 14.316 | |
| edgeRselection | 7.022 | 0.692 | 7.719 | |
| edgesToHubNetworks | 0.003 | 0.000 | 0.003 | |
| elasticNetFeatures | 0.269 | 0.151 | 24.270 | |
| elasticNetGLMinterface | 57.490 | 9.535 | 25.173 | |
| featureSetSummary | 0.009 | 0.005 | 0.014 | |
| fisherDiscriminant | 0.196 | 0.052 | 0.249 | |
| forestFeatures | 0.274 | 0.057 | 0.335 | |
| functionOrList-class | 0.016 | 0.005 | 0.022 | |
| functionOrNULL-class | 0.008 | 0.001 | 0.010 | |
| getLocationsAndScales | 0.072 | 0.012 | 0.084 | |
| integerOrNumeric-class | 0.030 | 0.005 | 0.036 | |
| interactorDifferences | 0.077 | 0.013 | 0.090 | |
| kTSPclassifier | 0.142 | 0.024 | 0.168 | |
| knnInterface | 0.065 | 0.009 | 0.075 | |
| leveneSelection | 2.835 | 0.340 | 3.207 | |
| likelihoodRatioSelection | 11.188 | 0.449 | 11.657 | |
| limmaSelection | 0.755 | 0.015 | 0.778 | |
| mixmodels | 1.340 | 0.098 | 1.451 | |
| naiveBayesKernel | 0.882 | 0.024 | 0.911 | |
| networkCorrelationsSelection | 0.410 | 0.002 | 0.413 | |
| pairsDifferencesSelection | 0.454 | 0.004 | 0.458 | |
| performancePlot | 0.456 | 0.020 | 0.477 | |
| plotFeatureClasses | 5.080 | 0.049 | 5.130 | |
| previousSelection | 5.767 | 3.965 | 4.936 | |
| previousTrained | 5.795 | 3.987 | 4.973 | |
| randomForestInterface | 0.432 | 0.091 | 0.523 | |
| rankingPlot | 4.610 | 1.011 | 5.383 | |
| runTest | 1.115 | 0.073 | 1.190 | |
| runTests | 23.815 | 9.557 | 12.790 | |
| samplesMetricMap | 7.762 | 0.570 | 8.363 | |
| selectionPlot | 5.352 | 0.822 | 6.072 | |
| subtractFromLocation | 0.002 | 0.001 | 0.004 | |